| |
Abstracts of Oral Presentations
The abstracts are split into the four sections in which they were presented, click on the headings below to jump to each section.
Section 1: The role of culture collections in the development of DNA barcodes and bioinformatics
Section 2: Current Curatorial Developments
Section 3: Natural Products and Biodiscovery
Section 4: Taxonomy, biodiversity and biogeography
Section 1: The role of culture collections in the development of DNA barcodes and bioinformatics
Chair: Dr. Guy Cochrane & Dr. Frithjof Küpper
Cochrane GR, Vaughan R, Faruque N & Birney E
The EMBL Nucleotide Archive: Genomics meets biodiversity
The EMBL Nucleotide Archive provides a repository of primary nucleotide sequence and annotation. Representing almost 130 million sequence entries from across the living world collected over more than a quarter of a century, the database continues to grow at an exponential rate. This growth is seen both in the number of records and in the increasing diversity of data sources – from biodiversity sequencing projects, through environmental genomics approaches to high-throughput genomes generated using the latest sequencing and assembly technologies. Along with collaborators DDBJ and GenBank, the EMBL Nucleotide Archive aims for comprehensive coverage of all publicly available sequence. A range of submission and retrieval tools are on offer. While the traditional focus of bioinformatics has been the genomes and transcriptomes of man and a small number of model organisms, the availability of affordable high-throughput sequencing to more and more researchers provides sequence coverage, albeit at low level, across a vast wealth of organisms, offering insights into the ecological make-up of communities and genetic diversity across time and space. While there exist in the order of 4,500 completed and ongoing genome-scale sequencing projects, as many as 300,000 species-level taxonomic nodes are already associated with nucleotide sequence in the archive. Key to exploiting data from these ‘low-coverage’ organisms is the integration of biomolecular data and tools with broader information already available for the organisms. One important connection to be made in this respect is between specimens in collections and nucleotide sequence data. The EMBL Nucleotide Archive has developed a number of structures under which specimens in collections can be explicitly connected to sequence and seeks to enrich cross-referencing to and from specimens in collections. In the talk, I will introduce the EMBL Nucleotide Archive and outline data and services, particularly those of importance for low-coverage organisms. Paying particular attention to work going on in collaboration with the Consortium for the Barcode of Life (CBoL) and others, I will discuss the integration of biomolecular data with collections.
EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Dawyndt P
Integrating algal culture collections within the StrainInfo.net bioportal
Biological research is inherently distributed in nature. With many researchers in different research institutes collecting and analyzing bits and pieces of biodiversity data, knowledge gained on the biotic world also has a tendency to become spread across the information jungle. As today’s upscaling of research projects often is hampered by the burden to integrate data extracted from several autonomous and heterogeneous information systems, the famous Newton quote “if I have seen a little further it is by standing on the shoulders of giants” is endangered to become rephrased as “If I can see no more, it is because giants were standing on my shoulders”. An immediate and important challenge that lies ahead of us is that of end-to-end scientific data management, from data acquisition and data integration, to data treatment, provenance and persistence. While advances in computing, and in particular scientific data management and application development environments for science will become important in the future, what is vitally more important and dramatic in its impact is the integration of new conceptual and technological tools from computer science into the life sciences. This integration is likely to accelerate key breakthroughs in science and benefits to society, from understanding biology and revolutionizing medicine and healthcare, and from understanding the universe to the origin of life, and understanding and helping to protect the life-support systems of Earth on which we all depend for our survival. The StrainInfo.net bioportal (www.straininfo.net) was established to stimulate this movement towards using multi-perspective integrated information in a broadened biological and clinical context. In particular, it concentrates on establishing automated ways to collect and integrate all information that is available about the organisms that were deposited into a global network of biological resource centres. Fully understanding the biology of an organism (or a population of organisms) requires taking a holistic approach wherein the phenotypic and genotypic traits of the organism are inspected in light of its ecological role and geographical spread. Moreover, only by having high quality information on those organisms we already know, we will be able to further explore and understand those regions of biodiversity that are yet unknown. Where the StrainInfo.net bioportal initially focused on microorganisms, we will open the discussion in this presentation whether its scope may be broadened towards including algae and protists. Based on an initial prototype, we will highlight some of the impediments against seamless data integration, propose possible ways of better collaboration and open the discussion on novel ways to exploit the vast amount of legacy data that drives phycology.
Department of Applied Mathematics and Computer Science, Krijgslaan 281 (S9), B-9000 Ghent, Belgium
Gugger M(1)), Tambosco J(1)), Rippka R(1)), Coursin T(1)), Laurent T(1)), Cruaud C(2), Gavory F(2), Weissenbach J(2) & Tandeau de Marsac N(1))
The Pasteur Culture Collection of Cyanobacteria (PCC): phylogenetic studies based on 16S rDNA sequences
Based on morphological characteristics, the Cyanobacteria can be organised into five major groups called subsections. As inferred by 16S rDNA sequence analyses, they constitute a robust monophyletic group within the Bacteria. Members of subsections IV and V form a distinct monophyletic clade, whereas those of subsections I-III are intermixed and highly divergent. Some representatives of subsections I and III may even occur in a same phylogenetic group. However, the global picture of cyanobacterial interrelationships is largely based on non-axenic isolates or on environmental samples for which relatively little information is available. To overcome the paucity of sequences representing the genetic diversity of axenic cyanobacteria, the 16S rRNA genes of 750 strains in the PCC were sequenced in order to establish their phylogenetic relationships. These organisms include 60 major morphotypes from diverse ecosystems and exhibit widely different physiological characteristics. Consequently, the new database should help to better define cyanobacterial Taxa and to place the phenotypic properties of the organisms into an evolutionary context.
(1))Institut Pasteur, Unité des Cyanobactéries, CNRS, URA2172, 75015 Paris, France
(2)Genoscope - Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, 91057 Evry Cedex, France
Brodie J
A brave new world? A review of the impact of DNA barcoding on the identification of benthic marine algae.
DNA barcoding - a short sequence of DNA from a standardized position in the genome used as a molecular diagnostic for species-level identification - remains controversial. However, the mitochondrial cytochrome c oxidase subunit 1 (cox1), the standard barcoding region for most groups of higher animals, is proving useful for the identification of red and brown benthic marine algae (seaweeds). This is particularly the case where intraspecific diversity has been overlooked in morphologically variable species (‘pseudocryptic’ diversity), or where Taxa are morphologically indistinguishable but genetically distinct (cryptic diversity). In the UK seaweed flora, hidden diversity has been discovered in approximately a third of the red algal species so far tested and there is evidence of incipient speciation in some of these. These results are leading to a shift in our understanding of algal biodiversity with implications for determining diversity, rarity, endemism and biogeography. In contrast to the red and brown algae, cox1 is not suitable for DNA barcoding in the green algae. I will review the use of DNA barcoding for the identification of seaweeds, with particular emphasis on examples of the red algae from our own work, and also put forward some suggestions for DNA barcoding the green algae.
Natural History Museum, Department of Botany, Cromwell Road, London, SW7 5BD, UK
Pröschold T(1), Seibel PN(2), Wolf M(2) & Coleman AW(3)
ITS-2 as universal DNA barcode marker for protists
DNA sequences are a powerful tool in systematics and molecular phylogeny of protists and have given new insights about the evolution of this group of organisms. However, it has not yet proven as rewarding for taxonomic categorization. DNA Barcoding has now been considered to close this gap. The goal of the International Barcoding Initiative is to find a single, universal, short DNA fragment, which is easy to sequence and leads to a clear species identification. The mitochondrial cytochrome oxidase subunit I (coxI) was proposed by the barcoding initiative and is mostly used by zoologists. However, for certain groups like higher plants and several groups of microalgae coxI is too conserved to separate organism at species level. In our study we used the second Internal Transcribed Spacer (ITS-2) of the nuclear ribosomal gene cistron. This locus has suggested a high degree of predictability across eukaryotes, is easy to sequence and its secondary structure is used for comparison at species, generic and higher taxonomic level. The main objection to the ITS-2 usage as barcode marker was the difficulties to align these sequences and the prediction of the secondary structure. With the help of the computer programme 4SALE and the ITS-2 Database of the University of Würzburg, as well as the easy recognition of two hallmarks in the secondary structure, these problems are resolved. Not only for protists, ITS-2 also gives additional information about the species concept. For example, compensatory base changes (CBCs) especially in the highly conserved region of Helix II and III correlate with the extent of sexual compatibility. A difference of even one CBC in this region predicts a total failure of crossing. This highly conserved region of ITS-2 can be consequently used as DNA Barcode marker for protists.
(1)Culture Collection of Algae and Protozoa, Scottish Association for Marine Science, Dunstaffnage Marine
Laboratory, Oban, Scotland
(2)Department of Bioinformatics, Biocenter, University of Würzburg, Germany
(3)Division of Biology and Medicine, Brown University, Providence, USA
Campbell CN(1), Saxon RJ(1), Day JG(1), Pröschold T(1), Küpper FC(1) & Gachon CMM(2)
Recent developments in bioinformatics at www.ccap.ac.uk
The Culture Collection of Algae and Protozoa (CCAP), the largest European protistan culture collection, is based at the Scottish Association for Marine Science near Oban, Scotland. The Collection comprises more than 2900 strains in the public domain, of which 1000 are marine algae, 1570 freshwater algae and 330 protozoa. The primary mission of CCAP is to maintain and distribute defined cultures and their associated information to its customers. The Collection has had an online catalogue for over 10 years (www.ccap.ac.uk) and this is currently expanding to provide a wide ranging protistan bioinformatics resource. In light of the increasing number of fully sequenced protists, the CCAP is striving to provide targeted services and support to workers involved in all aspects of genomic research. Our aim over the next two - five years is to increase the value of the collection by offering an integrated, up-to-date, easy-to-use resource that will provide curated information on our strain holdings. The website has already expanded to display images and has an enhanced search facility. We are now incorporating an increased range of data including: molecular information such as GenBank accession numbers; secondary structures and comprehensive reference lists of publications. In collaboration with other major Biological Resource Centres worldwide, we intend to build a hub providing access to both protistan cultures and their bioinformatics data. CCAP is supported by funding from the UK's Natural Environment Research Council.
(1)CCAP, Dunstaffnage Marine Laboratory, Oban, Argyll, PA37 1QA, UK
(2)Scottish Association for Marine Science, Dunstaffnage Marine Laboratory, Oban, Argyll, PA37 1QA, UK
Vaulot D, Probert I, Le Gall F, Rigaut-Jalabert F, Gourvil P & Marie D
The Roscoff Culture Collection (RCC): current status and perspectives
The Roscoff Culture Collection (RCC) currently holds over 1300 strains with emphasis on marine cyanobacteria (mainly Prochlorococcus and Synechococcus) and microalgae (mostly picoplankton from several classes, but also >350 strains of Haptophyta, mainly coccolithophores, recently transferred from the Algobank-Caen Collection). Most strains were isolated from the English Channel, the Mediterranean Sea, the Equatorial Pacific, the Tropical Atlantic, the Red Sea and the North Sea. The main strategic focus of the collection remains the isolation, maintenance, characterization and distribution of strains used for fundamental research. In this context, multiple strains of several Taxa (both prokaryote and eukaryote) that exhibit cryptic speciation and/or ecotype variability are maintained, as well as novel isolates from several algal classes. The collection includes the majority of marine cyanobacterial and microalgal strains for which the full genome sequencing is complete or in progress. A large fraction of strains are characterized based on morphological/ultrastructural features, SSU/LSU rDNA sequences and pigment analyses. Images (LM and EM) and taxonomic information on culture strains has been integrated into the Plankton*Net web resource (http://planktonnet.sb-roscoff.fr//index.php). The RCC website (http://www.sb-roscoff.fr/Phyto/RCC) has recently been redesigned to improve accessibility. Research priorities in coming years include targeted isolation of new strains (notably by flow cytometric cell sorting), cryopreservation and barcoding. In addition, screening of RCC strains for collaborative applied research in certain domains is envisaged. Planning is underway for transfer of the RCC to a dedicated laboratory facility at the Station Biologique in 2011.
Station Biologique de Roscoff, UMR 7144, CNRS et Université Pierre et Marie Curie, Place G. Tessier, 29682, Roscoff, France
Kasai F, Kawachi M, Erata M, Mori F, Yumoto K, Sato M & Ishimoto M
NIES-Collection: ex situ conservation of biodiversity and endangered algae in Japan
NIES-Collection holds 2527 strains that consist of various taxonomic groups in cyanobacteria, microalgae, freshwater macroalgae and protozoan including 295 genera and 609 species. Among them, 2096 strains are available. Most of them (78%) were collected within Japan, whereas 14% (3)01 strains) were collected from 35 countries/areas all over the world. Thus, we maintain diverse strains in terms of taxonomy as well as locality. NIES-Collection is also characterized by a large number of Microcystis strains (refer to the poster on Microcystis). As to habitats, however, most of NIES strains have been collected from ordinary habitats such as eutrophic lakes and inland sea, except for several isolated from hot springs such as Cyanidioschyzon merolae. NIES-Collection holds 400 additional strains, not available to the public. Half of them were collected from foreign countries such as Thailand, and China. We withhold distribution of those strains until the conclusion of MOU between relevant institutions in compliance with CBD. We also maintain 317 strains of endangered macroalgae (freshwater red and Charales algae). Several of them are endemic to Japan. Recently, habitats of these algae have decreased, and as a result, the number of populations has been reduced (refer to the poster on endangered algae in Japan).
Microbial Culture Collection, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
Jameson I(1),(2), Blackburn SI(1),(2),(3), Johnston C(1),(2), Frampton DMF(1),(2), Robert S(1),(2), Albinsson ME(1),(2),(3) & Bolch CJ(4)
The CSIRO Collection of Living Microalgae
The CSIRO Collection of Living Microalgae (http://www.cmar.csiro.au/microalgae/), Australia, maintains 800 strains and 140 genera, isolated from tropical to Antarctic waters representing the majority of marine and some freshwater microalgal classes. The Collection underpins research within the themes of environment, aquaculture and biotechnology. Studies of cultured strains under controlled conditions provide key information not only on phytoplankton dynamics but also feedback into strain characterization and optimizing the conditions for culture maintenance. Highly targeted studies of population genetics of Australian toxic dinoflagellates and cyanobacteria, is being complemented by barcoding initiatives (Canadian Barcode of Life Network) which, as one tool in genetic characterization, has strong support within Australia’s national collections. The CCLM is involved at a national level in strategic sampling of Australian microalgal biodiversity, improved taxonomic support as well as international collaborations. This strategy includes a future concerted move into cryopreservation. Existing web-based strain data in the CCLM will be incorporated into a biodiversity informatics framework readily accessible by key Australian agencies and with linkage into the Global Biodiversity Information Facility (GBIF). Supporting the Collection’s role in research and applications of Australian bioresources, the CSIRO Microalgae Supply Service provides microalgal strains to industry, government research organisations and universities in 50 countries for both research and industry applications.
1CSIRO Marine and Atmospheric Research
2CSIRO, GPO 1538, Hobart, Tasmania 7004, Australia
3Aquafin Cooperative Research Centre
4University of Tasmania, School of Aquaculture
Section 2: Current curatorial developments
Chair: Prof. Thomas Friedl
Benson EE(1), Day JG(2) & Harding K(1)
How Do Algae Survive Freezing? Exploring The Biophysical Basis of In Vivo and In Vitro Cryopreservation
In nature, algae and cyanobacteria have evolved strategies enabling them to survive extreme cold, ice and desiccation. Adaptations in the cryosphere and sea ice have taken several courses, determined by habitat dynamics and the need to tolerate frequent fluctuations in a changing environment, or seasonal changes in an otherwise stable one. A major survival factor is the ability to tolerate numerous freeze-thaw cycles, achieved by cryoprotective mechanisms, such as synthesizing compatible osmotica and antifreeze agents and adopting a poikilohydric life style. Cryopreservation of algae and cyanobacteria in culture collection cryobanks is dependent upon artificial cryoprotection, mediated through osmotic, colligative and vitrification-based protocols. Controlling water state and status is vital for surviving freezing, both in vivo and in vitro, especially through the migration of H2O and cryoprotectant molecules in and out of cells. However, water-conservation strategies that limit cell permeability during episodic desiccation in vivo might not be helpful for cryopreservation in vitro. This presentation conceptually explores the biophysical attributes of natural and artificial freeze and desiccation-tolerance in algae, with respect to optimizing cryoprotection in vitro, Differential Scanning Calorimetry (DSC) is evaluated as a tool for elucidating biophysical processes involved in cryoprotection using Euglena gracilis CCAP 1224/5Z as a model organism.
(1)Damar Research Scientists, Damar, Drum Road, Cuparmuir, Fife, KY15 5RJ, UK
(2)CCAP, Dunstaffnage Marine Laboratory, Dunbeg, Argyll, PA37 1QA, UK
Harding K(1), Müller J(2), Friedl T(2) & Day JG(3)
Cryopreservation, genetic stability and the concept of cryobionomics for Algal Culture Collections
The successful application of cryopreservation to algae within culture collections often utilises the widely acceptable traditional 2-step controlled rate methodology. Although, this may satisfactorily meet the normal service requirements of a collection it is not uncommon to find microalgae exhibiting different levels of survival following cryostorage. As cryopreservation is not universally applicable to all algae, this variable response to a single methodology within a collection is perhaps not too surprising, considering microalgae are taxonomically and morphologically diverse. These attributes and differential responses to cryopreservation contribute to the phenomenon of ‘recalcitrance’ preventing the wider application of cryostorage to significant sections of a collection. This restricted amenability may be overcome by using vitrification-based techniques that show promise as an alternative strategy to 2-step methods. A preliminary assessment was made using recalcitrant Euglena strains as ‘models’ to study their response to cryopreservation and identify critical factors in the alginate encapsulation-dehydration approach to cryostorage. Some extreme pre-treatment conditions showed detectable changes in Amplified Fragment Length Polymorphism (AFLP) patterns and growth characteristics following E. gracilis encapsulation-dehydration. A conceptual framework, cryobionomics will be presented to explore the significance of these changes to enable the preservation of difficult to freeze microalgae.
(1)Damar Research Scientists, Damar, Drum Road, Cuparmuir, Fife, KY15 5RJ, UK
(2)SAG, Universität Göttingen, Untere Karspüle 2, 37073, Göttingen, Germany
(3)CCAP, Dunstaffnage Marine Laboratory, Oban, Argyll, PA37 1QA, UK
Cox EJ
Culture collections and type specimens - what is their relevance to understanding and naming species and to resolving taxonomic and phylogenetic questions?
The development of molecular tools has revolutionized phylogenetic studies, but for micro-algal groups, their application usually relies on the availability of cultured material, while species delimitation and taxonomic arrangements are linked to published descriptions based on type specimens held in museums or herbaria. In both cases, conclusions must be based on available material and information. Thus, population studies and phylogenetic analyses use modern samples, while names are tied to historical material, and micro-algal type specimens are generally unavailable for molecular analysis. Integration of molecular data into taxonomy and systematics relies therefore on accurate identification of the cultured material. This talk will discuss the problems associated with these issues with particular reference to diatoms, whose taxonomy is highly developed, but whose species concepts are less well defined, and whose amenability to culturing varies. By examining and comparing the use and applicability of the different approaches, it will seek to show their relative strengths and weaknesses, and how to improve their interpretation and integration.
Department of Botany, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
Day JG(1), Pröschold T(1) & Friedl T(2)
Conservation of algal type material: approaches needed for 21st century science.
Under the current rules of the International Code for Botanical Nomenclature (ICBN; Vienna Code 2006), it is not permitted to deposit living specimens as type material. In fact the code states that the name should be attached to a designated type specimen in herbarium, or an image. Furthermore, any type material must be in a metabolically inactive state. One could debate whether this approach is truly suitable for science in the 21st century, where access to live specimens, DNA and/or bioinformatics data is of increasing importance. The protistan service culture collections are positioned to take on the role of conserving “live”, but metabolically inactive type specimens, by using cryopreservation. In addition to holding type specimens as reference material, they would be able to provide cultures to the scientific community on request. The service collections already hold significant numbers of authentic strains, derived from the original type material, e.g. CCAP hold >290 and the SAG hold ~430, and most now have the capability to cryopreserve microalgae. This paper discusses the suggestion that algal type specimens should be held as “live” cultures and investigates issues associated with: phenotypic and genotypic stability; quality standards, validation of methodologies and the logistics/ organisation that would be required to achieve this objective.
(1)CCAP, Dunstaffnage Marine Laboratory, Oban, Argyll, PA37 1QA, UK
(2)Georg-August-Universität, Albrecht-von-Haller-Institut für Pflanzenwissenschaften, Abt. Experimentelle Phykologie und Sammlung von Algenkulturen, Untere Karspüle 2, 37073, Göttingen, Germany
Surek B & Melkonian M
Culture Collection of Algae at the University of Cologne (CCAC): New cultivation techniques for microalgae
The Culture Collection of Algae at the University of Cologne (CCAC) was founded in 2001 and increased its number of clonal cultures to almost 1800 since then. Increasing the number of strains required the development of effective, time-saving culturing techniques in addition to the establishment of cryopreservation. CCAC has recently introduced a novel system for the stable long-term cultivation of microalgae, the Phycomat, based on the Twin-Layer Technology, which allows microalgae to grow in an immobilized state on ultrathin support layers. This new cultivating system, equipped with 96-well microtiter filter-plates, has been successfully used for selected strains of Chlorophyceae, Euglenophyceae and Zygnematophyceae, as well as for 46 strains of Symbiodinium spp. It allows growth of 96 different cultures in an area of less than 200 cm2. Exchange of culture medium or transfer of strains can be achieved simultaneously with minimum effort. A newly developed cover-lid, equipped with 96 LEDs and adjustable to light intensities ranging from 0.1 to 15 µMol/m2/s, is accurately positioned over the 96 wells of the microtiter plate. Each Phycomat thereby represents a "micro-growth-chamber", being independent of the light regime of the culture room. Introduction of LED lids allows Phycomats to be stacked, further reducing floor space significantly.
Botanisches Institut, Universität zu Köln, Gyrhofstraße 15, Köln, 50931, Germany
Bejoy T & Bolch CJS
Intra-specific variation in culture growth dynamics - genetic variation or environment?
Different clonal isolates of any algal species invariably exhibit different growth rates and culture dynamics even when maintained under identical culture conditions. Prevailing opinion is that these different phenotypes are predominantly an expression of genetic variation between individuals. Here we use cultures of the dinoflagellate Gymnodinium catenatum to investigate the relative importance of genotype and bacterial community composition on batch culture dynamics. Two G. catenatum cultures with markedly different growth dynamics (GCHU11 and GCDE08) were crossed to produce equivalent non-clonal progeny (resting cysts) that were surfaced-sterilised to remove all external bacteria. At germination, bacterial communities from either parent (or a mixture of both) were added to the germinated cells and allowed to establish a viable culture. Growth of the dinoflagellate and bacterial community was followed through a batch culture cycle and the growth dynamics compared with the two clonal parent cultures. Growth of the bacterial replacement cultures was consistently more similar to each other than to either parent culture and molecular (t-RFLP) analysis of the bacterial community indicated that, regardless of the community added at germination, a similar bacterial community was established in all progeny culture. Taken together with the growth data, this indicates that the growth dynamics in culture is predominantly a function of the bacterial community established with the dinoflagellate.
School of Aquaculture, University of Tasmania, Launceston, Tasmania, 7250, Australia
Section 3: Natural products and biodiscovery
Chair: Prof. Alan Harvey & Prof. Marcel Jaspars
Jaspars M
Streamlining the Biodiscovery Pipeline
The use of natural products by pharma, especially those of marine origin, is increasing again as the challenges that previously prevented their efficient incorporation into the drug discovery process are being met. This presentation will identify the major roadblocks in the biodiscovery pipeline and address ways in which these might be overcome. Many of these involve the integrated use of methods from taxonomy, chemistry, biochemistry, molecular genetics, screening technology and informatics. Aspects of collection, separation, assays, structure determination and sustainable supply of materials will be discussed. I will present short case studies from our own work on taxonomic assessment using metabonomics methodology and the use of heterologous expression to supply high value natural products.
Department of Chemistry, University of Aberdeen, Old Aberdeen, AB24 3UE, UK
Blackburn SI, Jameson I, Johnston C, Nichols CM, Frampton DMF, Mansour MP, Nichols PD, Robert S & Volkman JK
The CSIRO Collection of Living Microalgae: bioapplications
The CSIRO Collection of Living Microalgae (http://www.cmar.csiro.au/microalgae/) is a living bank of microalgae isolated from Australian waters from the tropics to Antarctica. Microalgal biodiversity is displayed in a range of bioactive compounds that have medical, human health, aqua-feed, and energy applications. Bioapplications of microalgal strains in the Collection and their genes are being explored as part of research undertaken in CSIRO National Research Flagships. CSIRO Wealth from Oceans Flagship is investigating exopolysaccharides (EPS) from microorganisms for new bioinspired adhesives, with microalgae from the Collection being screened for their EPS production, along with development of known targets of EPS-producing bacteria from the extreme Antarctic environment. Gene discovery in microalgae for biosynthesis of omega-3 long chain polyunsaturated fatty acids (LC-PUFA) that have an impressive range of human health benefits is one focus of the CSIRO Food Futures Flagship. The goal is to introduce the microalgal omega-3 pathway into genetically engineered crop plants, thus ensuring a sustainable source of omega-3 LC-PUFA for future global needs. The CSIRO Energy Transformed Flagship is investigating the potential of biodiesel from algae. High biomass cultivation of microalgae has the potential not only to produce oil and/or biomass for biofuels but also to mitigate CO2 and other greenhouse gases as part of photosynthesis and growth.
CSIRO Marine and Atmospheric Research, GPO Box 1538, Hobart, Tasmania, 7001, Australia
Chu WL(1), Kok YY(1), Lai PJ(2), Tan BK(1), Mohammed SM(1), Ling SN(1), Mak JW(1), Lim KC(2), Naidu R(3), Balraj P(2), Khoo ASB(2) & Phang SM(4)
Antiviral activity of microalgae extracts against Epstein Barr Virus (EBV)
Epstein-Barr virus (EBV) is a gamma-herpes virus associated with disorders such as Burkitt's lymphoma (BL) and nasopharyngeal carcinoma. The objectives of this study were to assess the antiviral activity of methanol extracts from the microalgae Ankistrodesmus convolutus UMACC 101 and Synechococcus elongatus UMACC 105 against EBV in lymphoblastoid cell lines and to elucidate the mechanism of action of such extracts. The antiviral activity of the microalgae extracts was assessed based on their inhibition on the release of viral particles in chemically induced lytic BL cells, namely Akata, B95-8 and P3HR-1 cells. In addition, the effect of the algae extracts on the expression of viral proteins LMP-1, EBNA-1 and ZEBRA in BL cells was investigated. The effect of the extracts on the interaction between the virus and cytoskeleton of the host cells was studied using immuno-fluorescence technique. Methanol extracts from Ankistrodesmus convolutes showed antiviral activity, decreasing 50% (EC50) of the cell- free viral load at 4.4 μg/mL The extracts also decreased the expression of the viral latent protein EBNA-1 from 40.1 % to 11.3% at 20 μg/mL The bioactivity of the extracts increased after fractionation by HPLC. The mechanism of action of the extracts was not due to their effect on the host cell cytoskeleton as revealed by the immuno-fluorescence studies.
(1)International Medical University, Sesama Centre, Plaza Komanwel, Bukit Jalil, 57000, Kuala Lumpur, Malaysia
(2)Department of Molecular Pathology, Institute of Medical Research, Jalan Pahang, Kuala Lumpur, Malaysia
(3)Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
(4)Institute of Biological Sciences, University Malaya, Kuala Lumpur, Malaysia
O'Higgins L
Incipient report of domoic acid production by four benthic diatom species under non-axenic batch culture conditions
Domoic acid (DA), a naturally occurring neuroexcitatory amino acid, was detected in late stationary phase batch cultures of three morphologically distinct Nitzschia species and one species of Amphora, tentatively identified as A. veneta. DA concentrations were confirmed in duplicate culture aliquots using a toxin-specific competitive Enzyme Linked Immunoabsorbent Assay kit (Biosense™) with a detection limit below 0.01 ng.DA.ml-1. Toxin concentrations were within ranges reported for known DA producers Pseudo-nitzschia seriata, P. multiseries and the newly described species, Nitzschia navis-varingica (Lundholm and Moestrup 2000) and reached a maximum of 3 pg.cell-1 in nitzschioid strain 1025. Minimum concentrations of 0.02 pg.cell-1 occurred in strain 1005, while concentrations of 2 pg.cell-1 are reported for amphoroid strain, 1026. All strains were non-axenic, isolated from inter-tidal sediments collected from Clew Bay, Co. Mayo and confirmed benthic by their adhesion to culture flask walls. Tentative species identifications were also made however due to the taxonomic difficulties associated with benthic microalgae, detailed morphologic and genetic characterization is required before speciation can be confirmed.
OSU Hatfield Marine Science Centre, 2030 SE Marine Science Drive, Newport, Oregon, 97365, USA
Harvey A
Natural products as a continuing source of inspiration for drug discovery
Natural products are the most consistently successful source of drug leads, but their use in industrial drug discovery has fallen out of favour. The difficulties, real and perceived, technical and political, in their use can be overcome. Several useful new lead compounds are in development and more can be expected from screening natural products. Despite the recognised structural diversity of natural products and their tremendous contribution to previous drug discovery research, pharmaceutical companies have generally cut back on their use of natural products in HTS. There seem to be several real and perceived problems associated with natural products in drug discovery. These are both technical and political. Natural products are frequently thought to be considerably more complex than synthetic ones. However, this is not necessarily so as revealed in the comparison of synthetic collections with natural products. Also, advances in separation chemistry and in techniques for analysis and structural elucidation of natural products make it much easier than before to work with natural products. Following up initial hits with extracts is no slower than scaling up and reconfirming hits made from a combinatorial library. In conclusion, the structural varieties of small molecules derived from natural products offer continuing promise for drug discovery campaigns. Many of the traditional difficulties associated with natural products have been overcome or sidestepped.
Strathclyde Innovations in Drug Research, University of Strathclyde, 27 Taylor Street, Glasgow, G4 0NR, UK
Stanley M(1) & Day JG(2)
Are Microalgae a Realistic Source of Biofuels?
The reduction in crude-oil stocks, an ever increasing demand for energy and concerns about global warming have all acted as stimuli to the on-going search for sustainable, renewable energy sources. The concept of microalgae lipids being used as a source of renewable energy is far from new but it is only now being taken seriously because of the escalating price of petroleum. To achieve the ultimate objective of economical, sustainable production of bio-fuels from algae, multidisciplinary, concerted, integrated research will be required to establish the knowledge base, culture systems and molecular tools required for optimising the production of industrially important oils and/or biomass. Presented here is an initial study, which aims to provide an analysis of each step in any possible algal bio-fuel production process.
(1)Scottish Association for Marine Science, Dunstaffnage Marine Laboratory, Oban, Argyll, PA37 1QA, UK
(2)CCAP, Dunstaffnage Marine Laboratory, Oban, Argyll, PA37 1QA, UK
Lloyd-Evans M
The role of the Bioscience for Business Knowledge Transfer Network in encouraging utilisation of bioresources
Culture Collections are important sources of biodiversity. They face many challenges including appropriate identification of samples, conservation and perpetuation in the collections in the form in which they arrived. There is also a pressing question of how collections are funded for long-term maintenance, survival and growth, especially at a time when there is growing interest in metagenomics analysis of undifferentiated mixed populations of organisms, a trend that clearly does not rely on maintenance of collections of organisms, but on retention of samples (water, soil, sediment cores etc) and libraries of cloned DNA or RNA. The funding must come from somewhere and in this less favourable environment, appropriate exploration and exploitation of culture collections is an important aspect of any strategy for survival. The Knowledge Transfer Networks are a programme of facilitating organizations established by the UK Technology Strategy Board to make sure that UK and international industries have access to the best resources that UK research has to offer, including culture collections. How the Bioscience for Business Knowledge Transfer Network envisages using culture collections as a source of novel biotechnology is the subject of this presentation.
Bioscience for Business, 45 St Barnabas Road, Cambridge, CB1 2BX, UK
Section 4: Taxonomy, biodiversity and biogeography
Chair: Dr. Eileen Cox
West J, West K, Pickett-Heaps J, Ackland J & Spurck T
Comparative cell motility of some 'bangiophycidean' and 'florideophycidean' red algae
Time-lapse video-microscopy reveals much about the biology of red algae. Spore movement is largely unknown. Cell motility and movement patterns in most red algae are varied: amoeboid and gliding are the most frequent types. Gliding spores are spherical with no visible external appendages that could cause movement. Amoeboid spores produce pseudopodia that appear active in movement. Velocity varies in different types of movement and in different isolates, ranging from 0.05 µm s-1 to 4 µm s-1. Most movement in red algae is substrate independent. Spores movie in and out of focus during filming and do not require substrate contact. During movement cells may have a sensory system that recognizes physical barriers.
Different red algae investigated:
Vegetative cells move. Porphyrideophyceae. Erythrolobus coxiae and Rhodellophyceae. Rhodella maculata, Dixoniella grisea, Neorhodella cyanea, Glaucosphaera vacuolata
Stylonematophyceae. Monospores glide. Stylonema alsidii, Purpureofilum apyrenoidigerum, Bangiopsis subsimplex, Rhodaphanes brevistipitata, Rhodosorus marinus
Compsopogonophyceae. Monospores mostly glide. Compsopogonales. Compsopogon caeruleus & Pulvinaster venetus Erythropeltidales. Erythrocladia irregularis, Sahlingia subintegra & Erythrotrichia spp. Rhodochaetales. Rhodochaete parvula
Bangiophyceae. Spores with pseudopodia & gliding. Bangiales. Porphyra pulchella
Florideophyceae Monospores with pseudopodia & gliding. Acrochaetiales. Acrochaetium spp. & Colaconematales. Colaconema tetrasporum. Monospores glide. Batrachospermales. Batrachospermum macrosporum. Spores glide. Ceramiales. Spyridia filamentosa, Antithamnion nipponicum, Bostrychia moritziana, Caloglossa vieillardii.
School of Botany, University of Melbourne, Parkville, VIC 3010, Australia
Krienitz L(1), Bock C(1), Luo W(1) & Pröschold T(2)
Systematics of coccoid green algae with the eyes of a morphologist, a limnologist and a molecular biologist
Coccoid green algae belong to the autotrophic microphytes which exhibit the highest biodiversity in freshwater habitats. Based on the introduction of molecular phylogenetic methods into systematics of coccoid green algae fundamental revisions of the concepts of higher taxonomical lineages of the Chlorophyta have been published during the last decades. Following these new phylogenetic conceptions the context of the orders which contain coccoid green algae has been considerably changed. Using examples of species and genera of the orders Chlorellales and Sphaeropleales, the controversial approaches of morphologists, limnologists and molecular biologists will be demonstrated. Morphologists use diacritical characteristics such as shape and size of cells and colonies, presence of cell wall sculptures, spines, pyrenoids, mucilage etc. Limnologists focus more on functional aspects of the Taxa such as edibility and their physiological and morphological responses to ecosystem interactions. Molecular biologists are looking for structural differences in the genome of the Taxa. It is widely accepted that non-homoplasious synapomorphies (NHS) and compensatory base changes (CBC) in the secondary structures of SSU and ITS-2 rDNA provide good tools for differentiation of species and genera. Combined approaches of morphological, ecophysiological and molecular-phylogenetical methods should help to elucidate a natural systematic conception of coccoid green algae.
(1)Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, D-16775 Stechlin, Germany
(2)CCAP, Dunstaffnage Marine Laboratory, Oban, Argyll, PA37 1QA, UK
Shubert E
Phenotypic plasticity in Desmodesmus as viewed with the SEM
Desmodesmus exhibits phenotypic plasticity in nature and in the laboratory. Yet, some species are too narrowly circumscribed and do not take into account morphological variability as viewed with the LM and the SEM. Several clones of Desmodesmus were cultured in different defined inorganic media and examined with LM and SEM. Clones produced spiny and spineless unicells, and spiny and spineless colonies. SEM analysis of wall ultrastructure produced a catalogue of characters that varied between clones cultured in a variety of nutrient conditions. When spiny unicells were compared to colonies and spiny colonies to spineless colonies, wart density was statistically different. Also, spine length varied within and between morphs. These results raise numerous taxonomic questions. How do we describe a plastic species whose characters are environmentally controlled, when environments change with time? How do we identify different morphological stages of the same organism from field collections? A polyphasic approach is proposed to delimit the species of Desmodesmus.
Department of Botany, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
Friedl T, Mohr K, Brinkmann N, Mudimu O & Hallman C
Identification and phylogeny of algae dominating biofilms: a challenge for algal systematics
Identification of algae from biofilm samples by culture and culture-independent methods was found not possible in many cases. This may be due to that diversity of biofilm algae is still poorly reflected in culture collections and sequence databases. Biofilms dominated by cyanobacteria and diatoms in stromatolite tufa of freshwater creeks, Biological Soil Crusts in southern African deserts as well as subaerial green algal biofilms on artificial hard substrates in urban environments were investigated here. From DNA extractions of biofilm material SSU rDNAs were amplified followed by cloning and sequencing or DGGE. Phylotypes, i.e. groups of highly similar sequences forming distinct clades, were recovered in phylogenetic analyses. Compared to a culture-independent approach, only a small fraction of the phylotypes was recovered by cultures. However, certain other phylotypes were retrieved only by culturing. This advocates combining both approaches assessing the diversity of algae from biofilms. In cases were no identification was possible by sequence comparisons, the algae need to be cultured and identified using traditional morphological features. However, this may be significantly hampered as the culture of biofilm algae often appeared to be difficult or even impossible. The phylotypes of biofilm algae may also comprise several cryptic species which cannot be distinguished by morphological features.
Georg-August-Universität, Albrecht-von-Haller-Institut für Pflanzenwissenschaften, Abt. Experimentelle Phykologie und Sammlung von Algenkulturen, Untere Karspüle 2, 37073, Göttingen, Germany
Kawai H, Hanyuda T, Müller DG & Yamagishi T
Genetic divergence of world-wide Ectocarpus populations based on mitochondria cox3 and nuclear Ocm3 gene sequences using KU-MACC culture strains
The Kobe University Macroalgal Culture Collection (KU-MACC) was established in 2003 as a section of the Kobe University Research Center for Inland Seas (KURCIS), and began to distribute cultures to the public in 2005. This collection is one of the research activities of KURCIS, but its development has been supported by the National BioResource Project (NBRP) of the Ministry of Education, Culture, Sports, Science and Technology (MEXT). KU-MACC principally holds macroalgae (Phaeophyceae, Rhodophyceae and Chlorophyceae), and preserves unialgal strains by maintaining vegetative thalli or by cryo-preservation in liquid nitrogen. More than 1,000 strains are preserved in total, and currently about 330 strains of about 160 species are available for distribution. By improvement of cryopreservation methods, about 30 % of the available strains are cryo-preserved. Especially, by the application of two-step cooling method for the reproductive cells, we have achieved considerably high survival rate of the Ectocarpus strains. Thereafter, currently about 90 Ectocarpus strains are cryo-preserved. Using those culture strains we have studied the genetic divergence of the world-wide Ectocarpus populations using mitochondria cox3 gene and nuclear mastigonema-related gene (Ocm3) sequences.
Kobe University Research Centre for Inland Seas, Rokkodai, Nadaku, Kobe, Japan
Swan S, Davidson K & Pete R
Monitoring harmful algal blooms in Scottish waters
SAMS operates the regulatory programme to monitor toxin producing phytoplankton in Scottish waters. This programme is intended to safeguard human health by minimizing the chances of harvesting, sale and consumption of shellfish contaminated with phytoplankton-derived biotoxins. Monitoring involves the weekly enumeration of eight species or genera of phytoplankton within water samples collected from 36 sites around the Scottish coast. Operation of the programme draws on both dedicated staff and members of CCAP based within SAMS. Data collected as part of the programme has allowed us to conduct various scientific studies looking at the factors that may influence harmful bloom initiation in Scottish waters.
Scottish Association for Marine Science, Dunstaffnage Marine Laboratory, Oban, Argyll, PA37 1QA
Mikhailyuk TI(1), Sluiman HJ(2), Rindi F(3), Massalski AK(4), Mudimu O(5) & Friedl T(5)
Interfilum and Klebsormidium are closely related streptophycean algae
Phylogenetic analysis of 18S rDNAs sequences have shown that the genus Interfilum belongs to the streptophycean lineage with a close relationship to the genus Klebsormidium. Recent studies have revealed a hitherto unknown species diversity of Interfilum including I. paradoxum, I. terricolum and I. massjukiae, as well as two strains probably representing new species (Mikhailyuk et al. in press). Phylogenetic analyses of ITS rDNA and rbcL sequences of representatives of Interfilum, Klebsormidium as well as the related genera Entransia and Hormidiella demonstrated that Interfilum is most closely related to a lineage formed by strains identified as Klebsormidium flaccidum. The best supported phylogeny implies that Interfilum is monophyletic whereas Klebsormidium is paraphyletic. However, alternative tree topologies in which Interfilum is the sister to a clade comprising all Klebsormidium species were not significantly worse according to Paired Sites tests. Additional molecular markers and taxon sampling may clarify this problem. These genera share many morphological characters: a chloroplast-microbody-nucleus structural complex in vegetative cells; a tendency of cell division in different planes; pseudo-bipartite cell walls. Both genera have the same type of cell division reminiscent of autospore formation giving rise to sarcinoid packets or pseudofilaments that often disintegrate easily into unicells.
(1)M.H. Kholodny Institute of Botany, National Academy of Sciences of Ukraine, Kiev, Ukraine
(2)Royal Botanic Garden Edinburgh, Edinburgh, UK
(3)Martin Ryan Institute, National University of Ireland, Galway, Ireland
(4)Pedagogical University, Institute of Biology, Kielce, Poland
(5)Experimental Phycology and SAG Culture Collection, University of Göttingen, Göttingen, Germany
Darienko T(1), Friedl T(2), Zufall-Roth E(2), Mudimu O(2), Beck A(3), Peters L(4), Schumann R(4) & Karsten U(4)
Taxonomic revision of a common aerophytic coccoid green alga previously assigned to Chlorella (Chlorophyta, Trebouxiophyceae)
Chlorella is a prominent example for a morphology-based genus of coccoid green algae that actually comprises several independent phylogenetic lineages of multiple origins as revealed by DNA sequence analyses. We focused in our studies on strains of SAG and CCAP designated as Chlorella saccharophila, and C. ellipsoidea. Our phylogenetic analyses of SSU rDNA sequence showed these strains being clearly separated from Chlorella vulgaris, type species of the genus, and its closest relatives, i.e. they were in a lineage of its own within the Trebouxiophyceae with C. luteoviridis being the next closest relative. Morphologically our isolates corresponded to authentic strains representing Chlorella trebouxioides and C. saccharophila. Kalina suggested the generic name Glaphyrella for C. saccharophila, however, this species was originally described by Krüger as Chlorothecium saccharophilum. This generic name is not valid according to the ICBN because it was previously use for a group of xanthophytes by Borzi. This was already recognized by several authors at the beginning of the 20th century, however, the nomenclatural status of Chlorella saccharophila and its closest relatives remains unresolved. In addition to C. saccharophila, this group also contains Chlorocloster engadinensis. Morphologically is this group characterized by its broadly ellipsoidal and asymmetric cell shape, but has no spherical cells. Most peculiar is the chloroplast, which is parietal in young stages and later becomes lobed. The chloroplast contains one large pyrenoid with a smooth appearance and is covered by small starch grains in many strains. Autospores within the sporangium are of unequal size. In congruence with the presence of three distinct ITS rDNA types within a clade representing strains of this group in SSU rDNA phylogenies and morphological features we distinguish three species, i.e. "Chlorella" trebouxioides, "C." saccharophila and "Chlorocloster" engadinensis. These species will be transferred to the new genus, when the nomenclatural status is resolved. Among the different isolates of "C." trebouxioides a considerable morphological variation in cell shape and chloroplast morphology was found, but it was not reflected in the rDNA sequence differences within the species. Another species of Chlorella, C. angustoellipsoidea, was found synonymous with G. trebouxioides. In all isolates studied were found a significant concentration of ribitol, a low molecular weight carbohydrate unusual for green algae, which is absent in Chlorella vulgaris. The function of ribitol as a compatible solute is probably an important component contributing to the desiccation tolerance of these species.
(1)M.H. Kholodny Institute of Botany, National Academy of Sciences of Ukraine, Kiev, Ukraine
(2)Experimental Phycology and SAG Culture Collection, University of Göttingen, Göttingen, Germany
(3)Botanische Staatssammlung München, D-80638 München, Germany
(4)University of Rostock, Institute of Biological Science, Applied Ecology, Rostock, Germany
 
Culture Collection of Algae and Protozoa (CCAP)
Dunstaffnage Marine Laboratory • Dunbeg • Oban • PA37 1QA • UK
Tel: +44 (0)1631 559000 • Fax: +44 (0)1631 559001 • Email: ccap@sams.ac.uk • Web: www.ccap.ac.uk
|
