Curriculum Vitae
I was born on 2 February 1952 in Groningen, the Netherlands. From 1971 – 1978 I studied biology at the Rijksuniversiteit Groningen (RUG, Groningen State University) and specialized in Microbial Ecology (Prof. Hans Veldkamp) and Molecular Genetics (Prof. Gerard Venema). For my master thesis I investigated interspecies H2 transfer between two anaerobic amino acid degrading bacteria, Clostridum cochlearium and Campylobacter sp. (1977) and the fate of heterologous transforming DNA in the genus Bacillus (1978). Further, I carried out literature studies on the effect of O2 on anaerobic bacteria (1978) and on the initiation of genetic recombination in bacteria (1978).
From 1 January 1979 I moved to Oldenburg, Germany, where I joined the group of geologist and geo-microbiologist Prof. Wolfgang E. Krumbein at the Geomicrobiology Division of the Carl-von-Ossietzky University. In 1983 I was appointed there as assistant professor ('Hochschulassistent') ‘Geomicrobiology’. In Oldenburg I became interested in the development of microbial mats and I studied extensively the cyanobacterial mats that developed in coastal sediments. In particular, I studied N2 fixation in mats formed by non-heterocystous cyanobacteria and investigated the strategies these organisms had evolved in order to protect the O2 sensitive enzyme. I was the first to isolate a filamentous non-heterocystous cyanobacterium capable of aerobic N2fixation in pure culture, showing that this organism separated N2 fixation temporally from oxygenic photosynthesis. Microbial mats turn frequently anoxic and therefore I investigated anaerobic metabolism in cyanobacteria. I discovered that mat-forming cyanobacteria are capable of fermentation of their intracellular carbon reserves and that the release of low-molecular fermentation products was a major factor that thrived other bacteria in the mat, notably sulfate-reducing bacteria. During this almost 10 years in Oldenburg, I wrote my PhD thesis ‘Nitrogen-fixing cyanobacteria in a marine microbial mat’, which I defended on 8 November 1985 at the ‘Rijksuniversiteit Groningen’ (promotor Prof. Hans Veldkamp).
On 1 March 1988 I moved to Amsterdam where I was tenured as associated professor in the Laboratory of Microbiology of the Universityof Amsterdam, the Netherlands. There I continued my studies on N2 fixation and anaerobic metabolism in cyanobacterial mats in coastal environments and to a lesser extend also in hypersaline ponds. Soon after I had moved to Amsterdam I became also interested in benthic diatoms. While cyanobacteria prefer fine sandy sediments, epipelic benthic diatoms thrive on fine muddy sediments and silt, forming biofilms on the surface of intertidal mudflats. It is hypothesized that these diatom biofilms contribute to the stability of intertidal muddy sediments. I started investigating the production of extracellular polymeric substances (EPS) by these benthic diatoms since it was conceived that EPS could act as glue that bind sediment particles. I showed that EPS production in benthic diatoms was partly the result of unbalanced growth. Two types of EPS were identified; one rich in acidic sugars and presumably responsible for the binding of sediment particles; the other rich in glucose which was used as a carbon reserve. Another line of interest that developed during the ‘Amsterdam period’ was the development and ecophysiology of cyanobacterial blooms. I studied extensively cyanobacterial blooms in the Baltic Sea and showed that the daily irradiance entering the water column is the critical factor for the development of a N2-fixing bloom. The diazotrophic cyanobacteria fix 10-20% of N2 in excess of their own demands and this is transferred to the non-diazotrophic picocyanobacteria.
From 1 June 1996 I was appointed Head of Department of Marine Microbiology of the Netherlands Institute of Ecology, Centre of Estuarine and Marine Ecology in Yerseke. My group focuses on the ecology, functional diversity and physiology of marine phototrophic microorganisms (mainly cyanobacteria and diatoms). Keywords of the research in my department include structure and development of phototrophic biofilms, acclimation of microalgal photosynthesis, N2 fixation in cyanobacteria, microbial mats and blooms and its interaction with photosynthesis and O2, exudation of EPS and oxidative stress. The department maintains a collection of cyanobacteria and benthic diatoms (CCY, Culture Collection Yerseke). The research of the department follows a large variety of different approaches including physiological, biochemical, biogeological, optical and other physical, molecular genetics and modelling.
From 1979 – 1996 I taught classes in ‘General Microbiology’, ‘Microbial Ecology’ and ‘Geomicrobiology’. I led several student excursions to the salt ponds of Guerande in France and to tropical marine, hypersaline and desert ecosystems in Israel and Sinai. I supervised numerous master students and 10 PhD Students.
In 1991 I obtained a Fulbright Fellowship and spent 4 months in the laboratory of Prof. Hans W. Paerl in the Institute of Marine Science of the University of North Carolina at Chapel Hill in Morehead City, NC, USA, working on microbial mats. In 2002 I was a visiting professor for 12 months in the Laboratory of Microbiology (Prof. Francisco Rodríguez Valera) at the Universidad Miguel Hernandez in San Juan de Alicante, Spain, supported by the Ministry of Education of the Spanish Government, studying genetic diversity of marine and hypersaline bacteria.
Expertise
Cyanobacteria
An important part of my research interests is in the field of the ecology, functional diversity and physiology of (marine) cyanobacteria. Cyanobacteria can be found in almost any environment. My research has focussed on benthic cyanobacteria that form microbial mats in coastal environments, and on planktonic cyanobacteria that form waterblooms in marine and semi-marine systems. To a lesser extent I have studied cyanobacteria from extreme and other unusual environments such as hypersaline ponds, hot springs and deserts. Aspects of cyanobacterial ecophysiology that I have studied include N2 fixation, photosynthesis, anaerobic metabolism and functional diversity. I maintain a large collection of (axenic) cyanobacteria that my group has isolated during our studies of a large variety of different environments.
Microbial mats and stromatolites
Microbial mats are vertically stratified communities of different functional groups of microorganisms. Microbial mats can be found in a variety of places that have in common extreme environmental conditions that exclude most other life, notably consumers. Examples include shallow coastal environments, hypersaline ponds, hot springs, cold and hot deserts. Coastal microbial mats are formed by cyanobacteria, purple- and colourless sulfur bacteria, sulfate reducing bacteria and a variety of other bacteria. These microbial mats are often considered as the modern analogues of communities that formed Precambrian stromatolites. Stromatolites are laminated biogenic reefs that are built by microorganisms. The laminations are usually the result of successive growth periods of the microbial mats. Stromatolites formed through calcification of the mats. Today, stromatolites are rare and most microbial mats do not lithify. Fossil stromatolites date back 3.5 billion years and represent the first witnesses of life on earth. The study of microbial mats and stromatolites is concerned with the interface between the geo- and biosphere and will provide us with clues of the evolution of both. The emphasis of my studies is on N2 fixation, photosynthesis, anaerobic metabolism, extracellular polymeric substances (EPS) and functional diversity.
Nitrogen fixation
I have studied N2 fixation in heterocystous and non-heterocystous cyanobacteria for many years. N2 fixation is an outstanding example of an anaerobic process and is incompatible with oxygenic photosynthesis. This paradox can be solved by studying the interactions with photosynthesis in heterocystous and non-heterocystous cyanobacteria and the mechanisms of protection of nitrogenase from oxygen. Heterocystous cyanobacteria seem to be excellent adapted for diazotrophic growth. It is therefore an enigma why these organisms are widely excluded from the marine environment. While blooms in the brackish Baltic Sea are composed of heterocystous species, non-heterocystous Trichodesmium spp. seem to be the dominant diazotrophs in the tropical oceans. Trichodesmium is considered globally the most important N2 fixing organism, responsible for perhaps as much as 50% of global N fixation. However, recently unicellular N2-fixing cyanobacteria have been discovered in the oceans and these organisms are probably very important. Similar paradoxical examples exist for microbial mats. Although the majority of coastal microbial mats are composed of non-heterocystous N2-fixing cyanobacteria, some systems are formed by heterocystous species, while again others are composed of both types. I investigate the mechanisms that underlie this diversity by using ecological, physiological and molecular genetic approaches. Furthermore, I hope to contribute to the explanation of the enigma of aerobic N2 fixation in unicellular cyanobacteria.
Diatom biofilms and sediment stabilization
While cyanobacterial mats develop on fine sandy sediments, intertidal mudflats are colonized by benthic epipelic diatoms. During the last decade these biofilms have enjoyed an increasing interest because their supposed involvement in the stabilization of intertidal muddy sediments. Erosion, deposition and transport of sediment in estuarine ecosystems have great ecological and economic consequences. Benthic diatoms exude extracellular polymeric substances (EPS) and my research has indicated that this may act as glue that change and stabilize the sediment. Moreover, diatom EPS may be one mechanism by which primary production is transported to higher trophic levels. Benthic diatoms may be responsible for as much as 50% of the primary production in estuaries. I have investigated the fate of this primary production by using natural abundance of stable isotopes (delta13C and delta15N). The interaction of EPS exudation with photosynthetic acclimation and nutrient availability is further studied in the framework of functional diversity of benthic diatoms and intertidal sediment characteristics. This research is intimately connected to a more general approach to understand the development of phototrophic biofilms. A spin-off of this research is the study of fouling of coatings by phototrophic microalgae and how to prevent this. The research aims at the understanding of the general patterns of the formation of phototrophic biofilms and how this knowledge can be used.
Extracellular polymeric substances (EPS)
Benthic diatoms and cyanobacteria may exude as much as 80% of the CO2 they fix as EPS which is predominantly composed of polysaccharides. I have shown that this exudation is partly the result of unbalanced growth due to nutrient limitations. The results show that in diatoms at least two operational fractions of EPS are produced, one of which is rich in acidic sugars and presumably responsible for binding sediment. The other type is rich in glucose and may be used by the diatoms as a storage carbon.
Anaerobic metabolism and osmoprotection
Other examples of my research include anaerobic metabolism and osmoregulation in cyanobacteria and diatoms. I have studied the role of dimethylsulfoniopropionate and its relation with dimethylsulfide production in benthic diatoms. I have investigated fermentation in a variety of benthic and planktonic cyanobacteria. In line with this research were investigations on hydrogen, sulfur and iron metabolism in benthic cyanobacteria as well as the production and function of poly-hydroxy-alkanoates in these organisms.
Culture collection
I maintain a culture collection of phototrophic microorganisms (Culture Collection Yerseke, CCY). This collection comprises currently over 150 cyanobacteria, more than 100 epipelic benthic diatoms and about 50 other microalgae. The majority of the strains are axenic and others are being purified. Most of the strains in our collection have been isolated in the course of our own research and they originate from a wide variety of different environments. A number of strains were obtained from other researchers or culture collections and are used as reference strains. In order to cope with the ever-increasing number of strains in the collection and to prevent artefacts from prolonged sub-cultivation, we are in the course of cryo-preserving all axenic strains at -180oC. We are currently describing the strains and producing a catalogue of them. The genomes of two cyanobacteria of our collection are currently being sequenced.
Projects
Greenbeach (ongoing)
Greenbeach is an ongoing project of the Department of Marine Microbiology that started in 2000. The project aims at the understanding of the greening of beaches such as is the case on the North Sea island of Schiermonnikoog in the north of the Netherlands. Cyanobacteria form microbial mats on these beaches and they consolidate the sand, cause net deposition of sediment and eventually transfer the beaches into a salt marsh type of environment. The microbial community is highly diverse and many heterocystous, non-heterocystous filamentous and unicellular cyanobacteria contribute to the high rates of N2 fixation that are observed in the mats. We investigate the microbial diversity of the mat and attempt to understand the role of the various groups of organisms in this ecosystem. Together with Prof. J.P. Zehr of the University of California in Santa Cruz (USA) we investigate the diversity of N2-fixing cyanobacteria by quantitative PCR of the nifH gene and study its expression by specific quantitative reverse-transcriptase PCR. We measure N2 fixation by using on-line acetylene reduction, a technique developed in our laboratory. Photosynthesis is studied by using O2 microelectrodes, PAM fluorescence using microfibers, membrane-inlet mass spectrometry and stable isotopes. This project is in part financed through the Schure-Beijerinck-Popping fund of the KNAW which also subsidized a TV programme in the series JOTA! (http://mmbase.teleacnot.nl/teleac/jota/aflevering.jsp?aflnr=38462).
Stromatolites (ongoing)
We started this project in 2003 through a collaboration with the US Research Initiative on Bahamian Stromatolites (RIBS) which is coordinated by Dr. Pamela Reid of the Rosenstiel School of Marine and Atmospheric Sciences in Miami, Florida (http://mgg.rsmas.miami.edu/groups/geomic/). We are interested in the processes that lead to calcification in microbial mats and the subsequent process of lithification. In this project, which was financially supported by the Schure-Beijerinck-Popping fund of the KNAW, we want to investigate N2 fixation using our on-line acetylene reduction technique.
DIVEPROD (ALW 832.11.003) (ongoing)
The project ‘Diversity – Productivity Relationships in Microphytobenthos’ is part of the Flemish-Dutch collaboration on sea research (VlaNeZO) and runs from 2002 - 2006. This is a joint research project between our group and the University of Ghent (Prof. Wim Vyverman) and the Technical University Delft (Dr. Gerard Muyzer). We investigate the diversity of benthic diatoms along a salinity gradient in the Westerscheldt estuary, by using classical taxonomical approaches and analyses of the 18S rRNA gene and the non-coding intergenic spacer between the genes coding for the large and small ribosomal subunits, and relating this diversity to function. With respect to the latter we investigate acclimation of photosynthesis, exudation of EPS and sediment stability. Dr. Veronique Créach is post-doc of this project.
MIRACLE (EU contract EVK3-CT-2002-00087) (2002 - 2005) (ongoing)
The project ‘Microbial Marine Communities Diversity: from Culture to Function’ is supported by the European Union (contract EVK3-CT-2002-00087) (http://miracle.umh.es). Miracle is coordinated by Prof. Francisco Rodríguez Valera of the Universidad Miguel Hernandez, Spain. Besides us other partners are the University of Barcelona, Spain; University of Bergen, Norway; University of Munich, Germany; CNRS and University of Montpellier, France; Plymouth Marine Laboratory, UK; BIOMAR, León, Spain. This project aims at the improvement of the methods for the cultivation of marine microbes by understanding the limitations and factors involved in the poor cultivability of these groups. Molecular tools and high through-put methodologies are extensively used to provide a better picture of what organisms are there, what conditions favour or hamper their growth in axenic cultures and, eventually, how to develop adequate methodologies to obtain pure cultures of these micro-organisms. Thomas Haverkamp and Ute Wollenzien are appointed on this project.
PHOBIA (EU contract QLRT-2001-01938) (2002 - 2005) (ongoing)
PHOBIA (Phototrophic Biofilms and their Applications) is a EU project (contract QLRT-2001-01938) of the Department of Marine Microbiology (http://www.itqb.unl.pt:1141/~webpages/mainpage/) coordinated by Dr. Jan Rijstenbil. This project studies the formation of biofilms by phototrophic microorganisms and investigates their structure and physiology. The goal is to develop a general concept of a phototrophic biofilm by an integrated modelling approach involving both structure and physiology. It is anticipated that the results of this research can be applied in waste water treatment plants, bioremediation and antifouling. Groups from the Technical University Delft, Netherlands; Marine Biological Laboratory, Helsingør, Denmark; UFZ, Magdeburg, Germany; ITQB Oeiras, Portugal; University of Rome Tor Vergata, Italy participate in this project. Dr. Marc Staal is post-doc in this project.
ALGINET (EU contract QLRT-2001-02132) (2002 - 2005) (ongoing)
Microalgae as Cell Factories for Chemical and Biochemical Products (ALGINET) (contract QLRT-2001-02132) (http://www.search-labs.com/Alginet/) is a European network of culture collections of microalgae, research groups and SME’s that wants to investigate the possibilities of biotechnological applications of microalgae. The Department of Marine Microbiology maintains a collection of cyanobacteria, diatoms and other microalgae (Culture Collection Yerseke, CCY, maintained by Ute Wollenzien).
New antifouling coatings with natural biocides for ship hulls (IZW99121B) (2000 - 2005) (ongoing)
This is a project in the framework of IOP Milieutechnologie / Zware Metalen (IZW99121) and the main goal is to set a first step in the development of a new environmentally safe antifouling coating for sea ships. The coatings applied today contain heavy metals with serious negative drawbacks for the environment. Therefore these coatings will soon be abandoned. Fouling is an important problem for ships that can increase the fuel use with as much as 30%. Hence, new antifouling coatings are urgently needed. We study the attachment of phototrophic micro-organisms (green algae, cyanobacteria and diatoms) and bacteria on a variety of coatings submersed in seawater. The formation of these biofilms and the role of extracellular polymeric substances (EPS) are studied by confocal laser scanning microscopy. Dr. Jody de Brouwer is post-doc of this project.
CLIMEROD (EU contract MAS3-PL97-1605) (1998 - 2001) (finished)
The project ‘The influence of climatic change on coastal sediment erosion’ was supported by the EU (contract MAS3-PL97-1605). This project was coordinated by dr. E. David of SOGREAH, France with other partners in Portugal, UK and France. It was a highly interdisciplinary project in which the effect of predicted climate changes on sediment characteristics, such as its rheology, were investigated. We investigated the effect of various parameters on exopolymer production by benthic diatoms and also characterized their rheological properties. (http://www.climerod.com).
ROBUST (EU contract ENV4-CT96-0218) (1993 - 1999) (finished)
The projects ‘Development and Fate of Cyanobacterial Blooms in the Baltic Sea' and ‘Baltic Sea Cyanobacteria. An Investigation of the Structure and Dynamics of Waterblooms of Cyanobacteria in the Baltic Sea– Responses to a Changing Environment’ (BASIC) were supported by the European Union (contracts EV5V-CT94-0404 and ENV4-CT97-0571) and coordinated by Dr. L.J. Stal. The project aimed at a basin wide, day and depth integrated calculation of photosynthesis and nitrogen fixation. We studied the role of different nutrients concomitantly with N2 fixation and photosynthesis. In addition, we studied the factors that determined the toxicity of the cyanobacterial blooms and determined the structure of the cyanobacterial community by molecular genetic techniques. Partners in this project were J.R. Gallon (Swansea), A.E. Walsby en P.K. Hayes (Bristol), B. Bergman (Stockholm), P. Albertano (Rome), K. Sivonen (Helsinki), K. von Bröckel (Kiel).
BASIC (EU contract ENV4-CT97-0571) (1994 - 1999) (finished)
The projects ‘Development and Fate of Cyanobacterial Blooms in the Baltic Sea' and ‘Baltic Sea Cyanobacteria. An Investigation of the Structure and Dynamics of Waterblooms of Cyanobacteria in the Baltic Sea– Responses to a Changing Environment’ (BASIC) were supported by the European Union (contracts EV5V-CT94-0404 and ENV4-CT97-0571) and coordinated by me. The project aimed at a basin wide, day and depth integrated calculation of photosynthesis and nitrogen fixation. We studied the role of different nutrients concomitantly with N2 fixation and photosynthesis. In addition, we studied the factors that determined the toxicity of the cyanobacterial blooms and determined the structure of the cyanobacterial community by molecular genetic techniques. Partners in this project were J.R. Gallon (Swansea), A.E. Walsby en P.K. Hayes (Bristol), B. Bergman (Stockholm), P. Albertano (Rome), K. Sivonen (Helsinki), K. von Bröckel (Kiel).
INTRMUD (EU contract MAS3-CT95-0022) (1996 - 1999) (finished)
The project ‘The morphological development of intertidal mudflats’ was supported by the European Union (contract MAS3-CT95-0022). This highly interdisciplinary project in which a large number of research groups from 4 countries were collaborating was coordinated by Prof. K. Dyer, University of Plymouth, UK. The objectives of the INTRMUD project were:
(i) to investigate the characteristics of intertidal mudflats in NW Europe in order to establish a classification which reflects the morphological effects of variations in such parameters as: tidal range and phase, wave climate, sediment physical and biological properties, biological community structure etc. (ii) to carry out experiments on a number of type mudflats, using harmonized methods, to quantify the processes, and their interactions, their ranges and timescales of variation, (iii) to formalize the relationships in statistical descriptions, and test the validity of the concepts by computer modelling, using experimental field data, (iv) to provide a basis of understanding which can be used in management of mudflats, in order to maintain ecological health, particularly under changing climatic, sea level, and anthropogenic pressures.
Selected Publications
Haverkamp THA, Schouten D, Doeleman M, Wollenzien U, Huisman J, Stal LJ 2008
Colorful microdiversity of Synechococcus strains (picocyanobacteria) isolated from the Baltic Sea
The ISME Journal on-line: doi:10.1038/ismej.2008.118
Publisher: http://www.nature.com/ismej
Full article: http://www.nature.com/ismej
Synechococcus is a cosmopolitan genus of picocyanobacteria living in the photic zone of freshwater and marine ecosystems. Here, we describe the isolation of 46 closely related picocyanobacterial strains from the Baltic Sea. The isolates showed considerable variation in their cell size and pigmentation phenotypes, yielding a colorful variety of red, pink and blue-green strains. These pigmentation phenotypes could not be differentiated on the basis of their 16S rRNA-internal transcribed spacer (ITS) sequences. Thirty-nine strains, designated BSea, possessed 16S rRNA-ITS sequences almost identical with Synechococcus strain WH5701. Despite their similar 16S rRNA-ITS sequences, the BSea strains separated into several different clusters when comparing the phycocyanin (cpcBA) operon. This separation was largely consistent with the phycobiliprotein composition of the different BSea strains. The majority of phycocyanin (PC)-rich Bsea strains clustered with WH5701. Remarkably, the phycoerythrin (PE)-rich strains of BSea formed an as yet unidentified cluster within the cpcBA phylogeny, distantly related to other PE-rich groups. Detailed analysis of the cpcBA operon using neighbour-net analysis indicated that the PE-rich BSea strains are probably endemic for the Baltic Sea. Comparison of the phylogenies obtained by the 16S rRNA-ITS, the cpcBA, and the concatenated 16S rRNA-ITS and cpcBA operon sequences revealed possible events of horizontal gene transfer among different Synechococcus lineages. Our results show that microdiversity is important in Synechococcus populations and that it can reflect extensive diversification of different pigmentation phenotypes into different ecological niches.
Reprint or PDF can be requested at library@nioo.knaw.nl
Acinas SG, Haverkamp THA, Huisman J, Stal LJ 2009
Phenotypic and genetic diversification of Pseudanabaena spp. (cyanobacteria)
The ISME Journal 3: 31-46
Publisher: www.nature.com/isme
Full article: http://www.nature.com/isme
Pseudanabaena species are poorly known filamentous bloom-forming cyanobacteria closely related to Limnothrix. We isolated 28 Pseudanabaena strains from the Baltic Sea (BS) and the Albufera de Valencia (AV; Spain). By combining phenotypic and genotypic approaches, the phylogeny, diversity and evolutionary diversification of these isolates were explored. Analysis of the in vivo absorption spectra of the Pseudanabaena strains revealed two coexisting pigmentation phenotypes: (i) phycocyanin-rich (PC-rich) strains and (ii) strains containing both PC and phycoerythrin (PE). Strains of the latter phenotype were all capable of complementary chromatic adaptation (CCA). About 65 kb of the Pseudanabaena genomes were sequenced through a multilocus sequencing approach including the sequencing of the16 and 23S rRNA genes, the ribosomal intergenic spacer (IGS), internal transcribed spacer 1 (ITS-1), the cpcBA operon encoding PC and the IGS between cpcA and cpcB. In addition, the presence of nifH, one of the structural genes of nitrogenase, was investigated. Sequence analysis of ITS and cpcBA-IGS allowed the differentiation between Pseudanabaena isolates exhibiting high levels of microdiversity. This multilocus sequencing approach revealed specific clusters for the BS, the AV and a mixed cluster with strains from both ecosystems. The latter comprised exclusively CCA phenotypes. The phylogenies of the 16 and 23S rRNA genes are consistent, but analysis of other loci indicated the loss of substructure, suggesting that the recombination between these loci has occurred. Our preliminary results on population genetic analyses of the PC genes suggest an evolutionary diversification of Pseudanabaena through purifying selection
Reprint or PDF can be requested at library@nioo.knaw.nl
Severin I, Stal LJ 2008
Light dependency of nitrogen fixation in a coastal cyanobacterial mat
The ISME Journal 2: 1077-1088
Full article: http://www.nature.com/ismej
The fixation of nitrogen in cyanobacterial mats situated along the littoral gradient on a Dutch barrier island was investigated by using a high-resolution online, near-real-time acetylene reduction assay. Light-response curves of nitrogenase activity yielded a variety of physiological parameters that changed during a day–night cycle. The fitted parameters were used to calculate nitrogen fixation from the incident natural irradiance over several days in two different mat types. Mats occurring in the higher regions of the littoral were composed of a diverse community of cyanobacteria, consisting of both heterocystous and non-heterocystous filamentous species, whereas closer to the low water mark the mats contained mainly non-heterocystous filamentous cyanobacteria. Although the daily cycles of nitrogenase activity differed considerably between the two types of mats, the daily integrated rates of nitrogen fixation were the same. Moreover, the daily integrated nitrogen fixation seemed to be independent from the daily incident photon flux. The measurements further suggest that different types of diazotrophic cyanobacteria become active at different times of the day and that the composition of the mat community affects maximal and daily patterns of nitrogenase activity. Notwithstanding the apparent light independence of nitrogen fixation, the lightresponse curves as well as light action spectra unequivocally showed that cyanobacteria were the predominant nitrogen-fixing organisms in these mats. It is concluded that the diversity of nitrogen-fixing cyanobacteria leads to an optimization of this process
Reprint or PDF can be requested at library@nioo.knaw.nl
Stal LJ 2008
Nitrogen fixation in cyanobacteria
Encyclopedia of Life Sciences 10.1002/9780470015902.a0021159
Publisher: John Wiley & Sons, Ltd: Chichester
Full article: http://www.els.net
Cyanobacteria are oxygenic photosynthetic bacteria that are widespread in marine, freshwater and terrestrial environments and many of them are capable of fixing atmospheric nitrogen. But ironically, nitrogenase, the enzyme that is responsible for the reduction of N2, is extremely sensitive to O2. Therefore, oxygenic photosynthesis and N2 fixation are not compatible. Hence, cyanobacteria had to evolve a variety of strategies circumventing this paradox allowing them to grow at the expense of N2, a ubiquitous source of nitrogen
Reprint or PDF can be requested at library@nioo.knaw.nl
Haverkamp T, Acinas SG, Doeleman M, Stomp M, Huisman J, Stal LJ 2008
Diversity and phylogeny of red and green picocyanobacteria inferred from their phycoerythrin and phycocyanin operons
Environmental Microbiology 10: 174-188
Publisher: http://www.wiley.com/bw/journal.asp?ref=1462-2912
Full article: http://www.wiley.com/bw/journal.asp?ref=1462-2912
Picocyanobacteria of the genus Synechococcus span a range of different colours, from red strains rich in phycoerythrin (PE) to green strains rich in phycocyanin (PC). Here, we show that coexistence of red and green picocyanobacteria in the Baltic Sea is widespread. The diversity and phylogeny of red and green picocyanobacteria was analysed using three different genes: 16S rRNA-ITS, the cpeBA operon of the red PE pigment and the cpcBA operon of the green PC pigment. Sequencing of 209 clones showed that Baltic Sea picocyanobacteria exhibit high levels of microdiversity. The partial nucleotide sequences of the cpcBA and cpeBA operons from the clone libraries of the Baltic Sea revealed two distinct phylogenetic clades: one clade containing mainly sequences from cultured PC-rich picocyanobacteria, while the other contains only sequences from cultivated PE-rich strains. A third clade of phycourobilin (PUB) containing strains of PE-rich Synechococcus spp. did not contain sequences from the Baltic Sea clone libraries. These findings differ from previously published phylogenies based on 16S rRNA gene analysis. Our data suggest that, in terms of their pigmentation, Synechococcus spp. represent three different lineages occupying different ecological niches in the underwater light spectrum. Strains from different lineages can coexist in light environments that overlap with their light absorption spectra
Reprint or PDF can be requested at library@nioo.knaw.nl
Kremer B, Kaźmierczak J, Stal LJ 2008
Calcium carbonate precipitation in cyanobacterial mats from sandy tidal flats of the North Sea
Geobiology 6: 46-56
Publisher: http://www.wiley.com/bw/journal.asp?ref=1472-4677
Full article: http://www.wiley.com/bw/journal.asp?ref=1472-4677
Precipitated calcium carbonate was found in annual cyanobacterial mats developing on the beaches of the North Sea barrier island Schiermonnikoog (the Netherlands). A variety of different calcium carbonate morphs were found in the cyanobacterial mucous secretions and identified by light- and scanning electron microscopy and X-ray diffraction. Most of the calcium carbonate seemed to be associated with degrading extracellular polymer. It is conceived that supersaturation of calcium carbonate resulted from the periodic evaporation of the mats and from the release of calcium from the cyanobacterial mucous as a result of its degradation. The analysis of the carbon stable isotopic composition of the calcium carbonate showed only a slight depletion of 13C, indicating that it did not in major part originated from the decomposition of organic matter. The delta 18O values of the calcium carbonate confirmed the temperature differences between spring and summer but excluded the possibility that excessive evaporative events controlled precipitation. The precipitation of calcium carbonate could represent a potential factor enhancing the stabilization of intertidal siliciclastic sediments through cementing the sand. The discovery of massive calcium carbonate precipitation in these cyanobacterial mats was unexpected and hitherto unknown
Reprint or PDF can be requested at library@nioo.knaw.nl
Stal LJ, Zehr JP 2008
Cyanobacterial nitrogen fixation in the ocean: diversity, regulation and ecology
The Cyanobacteria: Molecular Biology, Genomics and Evolution 423-446
Publisher: Caister Academic Press, Norfolk, UK
Nitrogen is an essential and major component of biomass. While virtually all life depends on combined forms of nitrogen that are usually limited in availability, some prokaryotes, including many groups of cyanobacteria, can use the ubiquitous atmospheric dinitrogen (N2). As photoautotrophic bacteria they can easily meet the energy demand that is required by nitrogenase, the enzyme that reduces N2 to NH3. However, nitrogenase is very sensitive to oxygen and the oxygenic cyanobacteria have evolved various strategies to cope with this paradox. Primary production in the ocean is generally considered to be limited by nitrogen. In recent years it has become clear that N2-fixing cyanobacteria are important in the nitrogen budget of the surface oceans. Estimates of N2 fixation indicate that approximately half of global N2 fixation occurs in the sea. N2 fixation is not distributed homogenously throughout the oceans. Pelagic diazotrophic cyanobacteria are only found in (sub)tropical oceans and are notably absent in temperate and colder seas. However, at lower salinities in estuaries and other brackish environments, N2-fixing cyanobacteria can be abundant. N2-fixing cyanobacteria are also abundant in benthic mats in coastal and aquatic environments all over the globe, including polar regions. This demonstrates that N2-fixing cyanobacteria are not excluded from temperate and cold marine environments, even though they are only found in the water column of warm oceans. In this chapter we will discuss these aspects and review the existing knowledge of the diversity of N2-fixing cyanobacteria and the factors that determine their global distribution
Reprint or PDF can be requested at library@nioo.knaw.nl
Stal LJ 2007
Cyanobacteria: diversity and versatility, clues to life in extreme environments
Extremophilic Algae, Cyanobacteria and non-photosynthetic Protists: From Prokaryotes to Astrobiology. Series: Cellular Origins, Life in Extreme Habitats and Astrobiology. 659-680
Publisher: Springer
Roeselers G, Stal LJ, van Loosdrecht MCM, Muyzer G 2007
Development of a PCR for the detection and identification of cyanobacterial nifD genes
Journal of Microbiological Methods 70: 550-556
Publisher: http://www.elsevier.com/locate/jmicmeth
Full article: http://www.elsevier.com/locate/jmicmeth
In this study we have designed degenerate primers after comparative analysis of nifD gene sequences from public databases, and developed a PCR protocol for the amplification of nifD sequences from cyanobacteria. The primers were tested on a variety of nitrogenase-containing and nitrogenase-lacking bacteria. By using this protocol, we amplified nifD sequences from DNA that was isolated from three phototrophic microbial communities. Denaturing gradient gel electrophoresis (DGGE) and clone library analysis of the nifD amplicons showed the presence of distinct groups of diazotrophic cyanobacteria in each of the investigated microbial communities. Phylogenetic trees constructed from the sequences of nifD gene fragments are congruent with those based on ribosomal RNA gene sequences
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Stomp M, Huisman J, Stal LJ, Matthijs HCP 2007
Colourful niches of phototrophic microorganisms shaped by vibrations of the water molecule
1: 271-282
Publisher: http://www.nature.com/ismej/
Full article: http://www.nature.com/ismej/
The photosynthetic pigments of phototrophic microorganisms cover different regions of the solar light spectrum. Utilization of the light spectrum can be interpreted in terms of classical niche theory, as the light spectrum offers opportunities for niche differentiation and allows coexistence of species absorbing different colors of light. However, which spectral niches are available for phototrophic microorganisms? Here, we show that the answer is hidden in the vibrations of the water molecule. Water molecules absorb light at specific wavebands that match the energy required for their stretching and bending vibrations. Although light absorption at these specific wavelengths appears only as subtle shoulders in the absorption spectrum of pure water, these subtle shoulders create large gaps in the underwater light spectrum due to the exponential nature of light attenuation. Model calculations show that the wavebands between these gaps define a series of distinct niches in the underwater light spectrum. Strikingly, these distinct spectral niches match the light absorption spectra of the major photosynthetic pigments on our planet. This suggests that vibrations of the water molecule have played a major role in the ecology and evolution of phototrophic microorganisms
Reprint or PDF can be requested at library@nioo.knaw.nl
Sahan E, Sabbe K, Créach V, Hernandez-Raquet G, Vyverman W, Stal LJ, Muyzer G 2007
Community structure and seasonal dynamics of diatom biofilms and associated grazers in intertidal mudflats
Aquatic Microbial Ecology 47: 253-266
Publisher: http://www.int-res.com/journals/ame/
Full article: http://www.int-res.com/journals/ame/
The composition and seasonal dynamics of biofilm-associated eukaryotic communities were analysed at the metre and kilometre scale along a salinity gradient in the Westerschelde estuary (The Netherlands), using microscopy and a genetic fingerprinting technique (PCR-DGGE). Microphytobenthic biomass, measured as chlorophyll a (chl a), varied seasonally over 2 orders of magnitude, being highest in spring. Communities were dominated by epipelic diatoms, in particular by members of the genus Navicula. In spring, a few smaller epipelic diatom species dominated during biomass peaks, while during the rest of the year, communities were more diverse and were characterised by larger species. The microphytobenthic community collapsed when grazers appeared, which happened concomitantly with a rise in temperature. Spring biomass development was associated with marked changes in porewater nutrient concentrations, especially towards the estuary mouth. In the DGGE data, diatoms, ciliates, amoebae, copepods, nematodes, annelids and platyhelminthes were detected. Ordination analysis of the species counts and DGGE data were largely congruent and indicated that on the scale of the whole estuary (i.e. km scale), taxonomic turnover in microphytobenthos composition was mainly associated with the salinity gradient. At smaller spatial scales, the position of sampling localities along the tidal exposure gradient appeared to be the main determinant of species turnover, in particular in the brackish reaches of the estuary
Reprint or PDF can be requested at library@nioo.knaw.nl
Stomp M, Huisman J, Vörös L, Pick FR, Laamanen M, Haverkamp T, Stal LJ 2007
Colorful coexistence of red and green pico-cyanobacteria in lakes and seas
Ecology Letters 10: 290-298
Publisher: http://www.wiley.com/bw/journal.asp?ref=1461-023x
Full article: http://www.wiley.com/bw/journal.asp?ref=1461-023x
Hutchinson’s paradox of the plankton inspired many studies on the mechanisms of species coexistence. Recent laboratory experiments showed that partitioning of white light allows stable coexistence of red and green picocyanobacteria. Here, we investigate to what extent these laboratory findings can be extrapolated to natural waters. We predict from a parameterized competition model that the underwater light colour of lakes and seas provides ample opportunities for coexistence of red and green phytoplankton species. To test this prediction, we sampled picocyanobacteria of 70 aquatic ecosystems, ranging from clear blue oceans to turbid brown peat lakes. As predicted, red picocyanobacteria dominated in clear waters, whereas green picocyanobacteria dominated in turbid waters. We found widespread coexistence of red and green picocyanobacteria in waters of intermediate turbidity. These field data support the hypothesis that niche differentiation along the light spectrum promotes phytoplankton biodiversity, thus providing a colourful solution to the paradox of the plankton
Reprint or PDF can be requested at library@nioo.knaw.nl
Staal M, te Lintel Hekkert S, Brummer GJ, Veldhuis M, Sikkens C, Persijn S, Stal LJ 2007
Nitrogen fixation along a north-south transect in the eastern Atlantic Ocean. Limnology and Oceanography
Limnology and Oceanography 52: 1305-1316
Nitrogenase activity, indicative of N2 fixation, was measured in the surface waters along a north–south transect in the eastern Atlantic Ocean, from Texel (The Netherlands, 53oN) to Cape Town (South Africa, 35oS) using a sensitive on-line, near real-time acetylene reduction assay. From the beginning of January to the end of February 2000 nitrogenase activity was detected in varying rates, but only between 14oN and 13oS latitudes. Dark incubations yielded an average activity of 2.2 (+/-2.4) umol m-2 d-1 N, but light increased the activity to 3.7 (+/- 2.9) umol m-2 d-1 N. However, nitrogenase activity in the light was sensitive to O2 doubling to 7.6 (+/- 12.7) umol m-2 d-1 N when the incubation was anaerobic. In the area where N2 fixation occurred, phosphate concentrations were fourfold lower than in the area where N2 fixation was absent, while silicate levels were higher. The water temperature in the area with N2 fixation was 28oC, while in the adjacent area the temperature was 3oC lower, which might have prevented the proliferation of diazotrophic cyanobacteria. Action spectra revealed that chlorophyll a, phycocyanin, and phycoerythrin are the light-harvesting pigments supporting nitrogenase activity. In one area in the northern latitudes, potential nitrogenase activity was highest during daytime, which is characteristic for Trichodesmium. In areas with a high potential nitrogenase activity, surface waters were dominated by a phycoerythrin-containing cyanobacterium. Since nitrogenase activities were highest at night, these cells may have been unicellular cyanobacteria like Crocosphaera
Reprint or PDF can be requested at library@nioo.knaw.nl
Staal M, Rabouille S, Stal LJ 2007
On the role of oxygen for nitrogen fixation in the marine cyanobacterium Trichodesmium sp.
Environmental Microbiology 9: 727-736
Publisher: http://www.wiley.com/bw/journal.asp?ref=1462-2912
Full article: http://www.wiley.com/bw/journal.asp?ref=1462-2912
The marine, non-heterocystous, filamentous cyanobacterium Trichodesmium shows a distinct diurnal pattern of nitrogenase activity. In an attempt to reveal the factors that control this pattern, a series of measurements were carried out using online acetylene reduction assay. Light response curves of nitrogenase were recorded applying various concentrations of oxygen. The effect of oxygen depended on the irradiance applied. Above a photon irradiance of 16 mmol m-2 s-1 nitrogenase activity was highest under anoxic conditions. Below this irradiance the presence of oxygen was required to achieve highest nitrogenase activity and in the dark 5% oxygen was optimal. At any oxygen concentration a photon irradiance of 100 mmol m-2 s-1 was saturating. When Trichodesmium was incubated in the dark, nitrogenase activity gradually decreased and this decline was higher at higher levels of oxygen. The activity recovered when the cells were subsequently incubated in the light. This recovery depended on oxygenic photosynthesis because it did not occur in the presence of DCMU [3-(3,4-dichlorophenyl)-1,1-dimethylurea]. Recovery of nitrogenase activity in the light was faster at low oxygen concentrations. The results showed that under aerobic conditions nitrogenase activity was limited by the availability of reducing equivalents suggesting a competition for electrons between nitrogenase and respiration
Reprint or PDF can be requested at library@nioo.knaw.nl
Stomp M, Huisman J, de Jongh F, Veraart A, Gerla D, Rijkeboer M, Ibelings BW, Wollenzien UIA & Stal LJ 2004
Adaptive divergence in pigment composition promotes phytoplankton biodiversity.
Nature 432: 104 – 107
Publisher: http://www.nature.com/nature/
The dazzling diversity of the phytoplankton has puzzled biologists for decades. The puzzle has been enlarged rather than solved by the progressive discovery of new phototrophic microorganisms in the oceans, including picocyanobacteria, pico-eukaryotes, and bacteriochlorophyll-based and rhodopsin-based phototrophic bacteria. Physiological and genomic studies suggest that natural selection promotes niche differentiation among these phototrophic microorganisms, particularly with respect to their photosynthetic characteristics. We have analysed competition for light between two closely related picocyanobacteria of the Synechococcus group that we isolated from the Baltic Sea. One of these two has a red colour because it contains the pigment phycoerythrin, whereas the other is blue-green because it contains high contents of the pigment phycocyanin. Here we report theory and competition experiments that reveal stable coexistence of the two picocyanobacteria, owing to partitioning of the light spectrum. Further competition experiments with a third marine cyanobacterium, capable of adapting its pigment composition, show that this species persists by investing in the pigment that absorbs the colour not used by its competitors. These results demonstrate the adaptive significance of divergence in pigment composition of phototrophic microorganisms, which allows an efficient utilization of light energy and favours species coexistence.
Reprint or PDF can be requested at library@nioo.knaw.nl
Riera P, Stal L & Nieuwenhuize J 2004
Utilization of food sources by invertebrates in a man-made intertidal ecosystem (Westerschelde, The Netherlands): a δ13C and δ15N study.
Journal of the Marine Biological Association 84: 323 – 326
Staal M, Meysman F, Stal LJ 2003
Temperature excludes N2-fixing heterocystous cyanobacteria in the tropical oceans
Nature 425: 504 – 507
Staal M, te Lintel-Hekkert S, Harren F, Stal LJ 2003
Light action spectra of nitrogenase activity in Baltic Sea cyanobacteria
Journal of Phycology 39: 668 – 677
de Brouwer JFC, de Deckere EMGT, Stal LJ 2003
Distribution of extracellular carbohydrates in three intertidal mudflats in Western Europe
Estuarine and Coastal Shelf Science 56: 313 – 324
Wolfstein K, de Brouwer JFC, Stal LJ 2002
Biochemical partitioning of photosynthetically fixed carbon by benthic diatoms during short-term incubations at different irradiances
Marine Ecology Progress Series 245: 21 – 31
de Brouwer JFC, Ruddy GK, Jones TER, Stal LJ 2002
Sorption of EPS to sediment particles and the effect on the rheology of sediment slurries
Biogeochemistry 61: 57 – 71
Riera P, Stal LJ, Nieuwenhuize J 2002
Delta 13C versus delta15N of co-occurring molluscs within a community dominated by Crassostrea gigas and Crepidula fornicata (Oosterschelde, The Netherlands).
Marine Ecology Progress Series 240: 291 – 295
Gallon JR, Evans AM, Jones DA, Albertano P, Congestri R, Bergman B, Gundersen K, Orcutt KM, von Bröckel K, Fritsche P, Meyerhöfer M, Nachtigall K, Ohlendieck U, te Lintel Hekkert S, Sivonen K, Repka S, Stal LJ, Staal M 2002
Maximum rates of N2 fixation and primary production are out of phase in a developing cyanobacterial bloom in the Baltic Sea
Limnology and Oceanography 47: 1514 – 1521
Karl D, Michaels A, Bergman B, Capone D, Carpenter E, Letelier R, Lipschultz F, Paerl H, Sigman D, Stal L 2002
Nitrogen fixation in the world’s oceans
Biogeochemistry 57/58: 47 – 98
van Bergeijk SA, Schönefeldt K, Stal LJ, Huisman J 2002
Production and consumption of dimethylsulfide (DMS) and dimethylsulfoniopropionate (DMSP) in a diatom-dominated intertidal sediment
Marine Ecology Progress Series 231: 37-46
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