Discovered in the late 1970's in the Atlantic ocean, picophytoplankton is a group of tiny unicellular organisms performing photosynthesis, a biological process during which the light energy is used to convert carbonic gas (CO2) into carbohydrates, one of the essential foods for living organisms. This process releases oxygen (O2) and its apparition some 2.5 Ma ago has been a key factor for the development of many kinds of living forms on Earth.
The term phytoplankton comes from the Greek words “phyton” meaning plant and “plagktos” meaning wandering, because these organisms are taken along marine currents. The prefix "pico" probably comes from a Spanish word and means "tiny". The picophytoplankton is constituted of both evolved organisms, called "eukaryotes", which have well-defined nuclei and organelles (such as mitochondria or plastids) and of more primitive organisms, called "prokaryotes", in which the cell components (DNA, ribosomes, membranes, etc.) are not separated into defined compartments. More precisely, the prokaryotic component of picophytoplankton is composed of "cyanobacteria" ("cyano" means blue-green, referring to the colour of the first of these organisms to have been studied).
In oceanic waters, cyanobacteria comprise only two main genera: Synechococcus and Prochlorococcus. With concentrations ranging from several thousands to several hundreds of thousands per millilitres of seawater, these organisms dominate biomass and production in wide expanses of the ocean, thus playing a key role in global elemental cycles such as the carbon cycle. Prochlorococcus alone contributes for about 50% of the chlorophyll in the central, nutrient-poor parts of the ocean, suggesting that an important portion of the O2 we are breathing may come from these extremely small organisms. Because of their central role in the mediation of fluxes of matter and energy, studying picophytoplankton biology and ecology appears as an essential step in the better understanding and prediction of the effects of global changes.
Synechococcus and Prochlorochoccus
Credit photograph of Synechococcus: Marine photosynthetic prokaryotes group in the Station Biologique de Roscoff
Credit photograph of Prochlorococcus: http://www.cns.fr/externe/Francais/Projets/Projet_DR/organisme_DR.html
Thanks to the development of genomics, research in this field has advanced considerably. Indeed with the sequencing of some 20 full genomes of Prochlorococcus and Synechococcus, scientists are now starting to understand the intimate functioning of those organisms. Furthermore, comparing these genomes allows to understand the mechanisms by which those organisms have adapted to specific ecological niches in the ocean. Phylogenomics which is the phylogenetic study of complete genomes (instead of single genes as is usually done) also provides unprecedent insights into the evolution of this very ancient group.
Going towards the preservation of biodiversity starts by being able to acknowledge the incredible variety of species that are present in the environment. Making the inventory of marine microbial organisms has been facilitated by the development of the high-throughput analysis techniques. In fact, during the past few years, scientists have been able to determine new species of Prochlorococcus and Synechococcus (which are sister groups in the phylogenic tree of life) contributing to making us understand what a great diversity of life forms exist in the ocean.
Worldwide, many different laboratories are studying biological aspects of these cyanobacteria that could be affected by stress potentially engendered by global changes.
For instance, within the MGE network, the British are mainly interested in the metabolism of phosphate and the Israeli by the nitrogen metabolism, both of these being key elements in Ecology. As stress caused by ultraviolet (U.V.) radiations is also central in today’s preoccupations, the study of the metabolism that are linked to this kind of stress is being studied in the Station Biologique de Roscoff (partner # 2).
Studying the biology of these organisms allows to answer many fundamental questions in basic research such as the function of genes, what they code for or what they control. The "Marine Photosynthetic Prokaryotes" team of the Station Biologique de Roscoff is particularly interested in the genes that code for light-harvesting antennae and their regulation by light.
Synechococcus light harvesting antennae or phycobilisome
http://www.sb-roscoff.fr/Phyto/index.php?option=com_content&task=view&id=91&Itemid=153
These antennae (called "phycobilisomes" in Synechococcus) are composed of pigment-proteins complexes arranged in such a way to capture light with a high efficiency. Pigments that are bound to antenna systems may have very different colours (such as green, blue, pink or orange) and this will determine the wavelengths of the solar spectrum that cells can efficiently harvest in the oceanic waters.
Antenna systems are interesting in many aspects. Indeed, they constitute the most variable parts of the photosynthetic machinery. Synechococcus or Prochlorococcus have totally different antenna systems and each genus itself displays a large amount of variability in the structure of these complexes. In fact, scientists are hypothesizing that the evolution of some of the genes coding for those antennae may be different from the rest of the genome, since they might be transferred "laterally" (i.e. by direct transmission of genes during conjugation) from one strain to another. This would allow genotypes to rapidly adapt to new light niches, when they are transported e.g. from offshore blue waters to onshore green waters or vice versa.
It is interesting to point out that the coastal waters are green not only because presence of particles of terrestrial origin but also because they contain so much phytoplankton. Further from the coasts, there is much less chlorophyll in the water and it is therefore blue which is water’s natural colour.
Some species of Synechococcus, called chromatic adaptors, even have the ability to slightly change the ratio of pigments bound to their antennae in order to match natural changes in light quality occurring in their environment. These species can therefore live at different depths and places in the ocean.
As part of basic research, genes involved in the control of the biological clock of these organisms is also being studied at the Station Biologique de Roscoff. In fact, this biological clock is present in all living organisms and it is therefore interesting to see whether the same genes are involved in its regulation and how such a phenomenon is possible.
Research in this field has been developed considerably since the study of the whole genome of these organisms is possible (see genomics). These organisms are in fact privileged targets for sequencing projects as their genomes are very small, containing less than 2.5 millions of pairs of bases. The smallest eukaryotic alga, Ostreococcus has a genome that is already 4 to 5 times bigger (10.6 mega base pairs). Supported by MGE, in a flagship project called SYNCHIPS the different partners working on these organisms have been able to get about 20 genomes of different strains of Synechococcus and Prochlorococcus sequenced which is quite extraordinary. This great amount of data is now being used by different laboratories interested in these cyanobacteria.
Phylogenomics has been greatly facilitated by the invention in this purpose of a computer program by Alexis Dufresne in the Station Biologique de Roscoff. It compares the genomes automatically and finds the resembling sequences. Transcriptomics is being developed also in SYNCHIPS. For a few selected species, several short sequence (2-4 nucleotides) are being defined for each interesting gene and will be put on chips (microarrays). These will be used to see the level of expression of the genes in different conditions: different UV light exposure, lack of phosphor or nitrogen in the growth media.
Transposition Mutagenesis is also being developed. It is a high throughput method for determining mutants which they can’t resist to certain conditions of stress and for analysizing them. This enables to identify the genes indispensable for the organism to resist to these stresses. Thanks to the chip developed by SYNCHIPS, these genes will be identified more easily.
Targeted mutagenesis is also being used in the Station Biologique de Roscoff in order to study the “antennas genes” more specifically.
Biochemistry is another approach that is being used to study the proteins composing the antennas. These proteins will be isolated thanks to a type of chromatography (after having broken up the cell, the proteins will be separates from each other through a gel containing a pH gradient. The colour of the pigment attached to the proteins of the antenna allows seeing them easily and the specific proteins of interest are extracted with a robot).
At a physiological level, photosynthesis, the cellular cycle, etc… are also being looked at by techniques as flow cytometry (go to: http://www.facslab.unibe.ch/flow.html ). This technique is commonly used to count cells and check their physiological state (i.e. DNA content).
To study how the bacteria biologic clock is regulated, scientists are using a machine called the Cyclostat which simulates the day and night cycle. By putting the organism from a continuous light to a day/night alternation, there will be a laps of time during which the bacteria will remember its biological clock. This precise period of time will be very interesting to study as it will allow researchers to see which genes are turned on to allow the bacteria to have this biological clock. The expressed genetic material at different period of time will be compared between each other by using microarrays.
The SYNCHIPs project (which stands for Synechococcus Chips) is a consortium within MGE regrouping 4 partners from Germany, Israel, Great Britain and France). The sequencing of the different genomes have been done by different platforms, the Genoscope, the Joint Genome Institute in Walnut Creak, California (USA) and the Joint Technology Center in Rockville, Maryland (USA), a huge sequencing platform that is part of the J. Craig Venter Institute.
Research that is going on in the different laboratories of the network, Marine Genomics Europe, will be able to bring many answers to important ecological questions such as: What will become of these organisms in the future as a consequence of the hole in the ozone layer? What will be the impact of the increasing rate of pollutants present in the ocean?
Many interesting molecules can be found in these organisms such as UV resistant proteins that could be used in sunscreen lotions.
However, the aim of the researches at the Station Biologique de Roscoff is more fundamental. The discovery of Prochlorococcus in 1988 by P. Chisholm has considerably changed the way scientists saw oceanography revealing an unsuspected enormous biomass. Knowing their genomes and going towards understanding their physiology through different types of approaches have already enabled scientists to discover many new aspects of these organisms’ biology. For example, different ecotypes of Prochlorococcus adapted to different depths in the ocean have been identified revealing tremendous biological diversity within a same species and impressive strategies of adaptation.
Contributed by Stephanie Ries and Frederic Partensky
