Lucas J. Stal

Dinitrogen fixation in the world's oceans

The surface water of themarine environment has traditionally beenviewed as a nitrogen (N) limited habitat, andthis has guided the development of conceptualbiogeochemical models focusing largely on thereservoir of nitrate as the critical source ofN to sustain primary productivity. However,selected groups of Bacteria, includingcyanobacteria, and Archaea canutilize dinitrogen (N2) as an alternativeN source. In the marine environment, thesemicroorganisms can have profound effects on netcommunity production processes and can impactthe coupling of C-N-P cycles as well as the netoceanic sequestration of atmospheric carbondioxide. As one component of an integrated ‘Nitrogen Transport and Transformations’ project, we have begun to re-assess ourunderstanding of (1) the biotic sources andrates of N2 fixation in the worldsoceans, (2) the major controls on rates ofoceanic N2 fixation, (3) the significanceof this N2 fixation for the global carboncycle and (4) the role of human activities inthe alteration of oceanic N2 fixation. Preliminary results indicate that rates ofN2 fixation, especially in subtropical andtropical open ocean habitats, have a major rolein the global marine N budget. Iron (Fe)bioavailability appears to be an importantcontrol and is, therefore, critical inextrapolation to global rates of N2fixation. Anthropogenic perturbations mayalter N2 fixation in coastal environmentsthrough habitat destruction and eutrophication,and open ocean N2 fixation may be enhancedby warming and increased stratification of theupper water column. Global anthropogenic andclimatic changes may also affect N2fixation rates, for example by altering dustinputs (i.e. Fe) or by expansion ofsubtropical boundaries. Some recent estimatesof global ocean N2 fixation are in therange of 100–200 Tg N (1–2 × 1014 g N)yr−1, but have large uncertainties. Theseestimates are nearly an order of magnitudegreater than historical, pre-1980 estimates,but approach modern estimates of oceanicdenitrification.

Comparative structure, primary production and biogenic stabilization of cohesive and non-cohesive marine sediments inhabited by microphytobenthos

The microstructure, rate of primary production and erodibility of noncohesive and cohesive marine sediments colonized by autotrophic microbial assemblages were investigated. Microbial development on non-cohesive sediments (Island of Texel, The Netherlands) formed millimetre-thick stratified mats. A surface sheath of extracellular polymeric substances (EPS) was visible on these mats; diatoms dominated the surface 500 μm with an underlying layer of cyanobacteria, mainly Microcoleus chthonoplastes. In comparison, biofilms on cohesive sediment (Bristol Channel, U.K.) were relatively thin (100 μm) and unstratified. The microspatial distribution of the algal biomass was confirmed by measurements of oxygen evolution and rates of primary production using oxygen micro-electrodes. While gross primary production was greater in the non-cohesive sediments, peak rates of photosynthetic activity and algal biomass were similar for the two sites. The erodibility of colonized areas was measured and the mechanisms of biogenic stabilization were examined by low-temperature scanning electron microscopy (LTSEM). Cohesive sediment stabilization was purely by the secretion of EPS while both EPS binding and network formation by cyanobacteria were visualized within the non-cohesive sediments. Areas where mat and biofilm systems were visible were more resistant to sediment erosion than adjacent areas without biofilm development. Direct comparison between biogenic effects at the two sites must be treated with caution because of the different nature of the sediments but the index of biogenic stabilization for both sites is reported. The stability of the non-cohesive sediments was greatly increased by the presence of a microbial mat. The hydration state of the EPS matrix was considered to have a potential effect on the critical erosion threshold of the sediments.

Adaptive divergence in pigment composition promotes phytoplankton biodiversity

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.

Analysis of a marine phototrophic biofilm by confocal laser scanning microscopy using the new image quantification software PHLIP

BackgroundConfocal laser scanning microscopy (CLSM) is the method of choice to study interfacial biofilms and acquires time-resolved three-dimensional data of the biofilm structure. CLSM can be used in a multi-channel modus where the different channels map individual biofilm components. This communication presents a novel image quantification tool, PHLIP, for the quantitative analysis of large amounts of multichannel CLSM data in an automated way. PHLIP can be freely downloaded from http://phlip.sourceforge.netResultsPHLIP is an open source public license Matlab toolbox that includes functions for CLSM imaging data handling and ten image analysis operations describing various aspects of biofilm morphology. The use of PHLIP is here demonstrated by a study of the development of a natural marine phototrophic biofilm. It is shown how the examination of the individual biofilm components using the multi-channel capability of PHLIP allowed the description of the dynamic spatial and temporal separation of diatoms, bacteria and organic and inorganic matter during the shift from a bacteria-dominated to a diatom-dominated phototrophic biofilm. Reflection images and weight measurements complementing the PHLIP analyses suggest that a large part of the biofilm mass consisted of inorganic mineral material.ConclusionThe presented case study reveals new insight into the temporal development of a phototrophic biofilm where multi-channel imaging allowed to parallel monitor the dynamics of the individual biofilm components over time. This application of PHLIP presents the power of biofilm image analysis by multi-channel CLSM software and demonstrates the importance of PHLIP for the scientific community as a flexible and extendable image analysis platform for automated image processing.

Isolation and characterization of extracellular polysaccharides from the epipelic diatoms Cylindrotheca closterium and Navicula salinarum

The production and composition of extracellular polymeric substances (EPS) in axenic batch cultures of the benthic marine epipelic diatoms Navicula salinarum and Cylindrotheca closterium were investigated. EPS was secreted into the medium and the bulk was loosely associated with the cells. Neither N. salinarum nor C. closterium formed a well-defined polysaccharide capsule. EPS of both N. salinarum and C. closterium consisted predominantly of polysaccharide but small quantities of protein were present as well. EPS also contained uronic acids and SO4 −2 groups. Analysis of monosaccharides using gas chromatography showed that for both species glucose and xylose were the main constituents, but several other monosaccharides were present in smaller quantities. Two fractions of EPS were distinguished: a small amount was secreted into the medium and a second fraction was extracted in water at 30 °C. For both species the two fractions differed somewhat in composition, indicating that they represented two different...

Interplay between biology and sedimentology in a mudflat (Biezelingse Ham, Westerschelde, The Netherlands)

Abstract The aim of this research was to investigate the importance of biological processes on the sediment characteristics and the morphology of a mudflat in the Westerschelde (The Netherlands). For this purpose, a transect in the Biezelingse Ham mudflat was sampled on a monthly basis. In spring, the muddy part of the mudflat was dominated by a biofilm of microphytobenthos that altered the morphology of the mudflat and resulted in a two-fold increase in sediment stability. The biofilm also bound fine-grained sediment that was deposited. From June onwards, wind generated waves dominated the conditions at the mudflat which resulted in the disappearance of diatom biofilms, and caused a gradual erosion of the mudflat. During this period, meio- and macrofauna densities increased from which it was concluded that the hydrodynamic forces did not have a big impact on these communities. Spatial variations in sediment characteristics, morphology and biology were observed between stations 1 and 2 on the one hand and station 3 on the other. This resulted in different responses to the changing conditions on the mudflat. In general, the results from this field study indicate that sedimentology and biology, interact in a complex manner with the hydrodynamic regime both on a temporal as well as on a spatial scale.

Exopolysaccharide production by the epipelic diatom Cylindrotheca closterium: effects of nutrient conditions

During the stationary phase of a batch culture of the epipelic diatom Cylindrotheca closterium, accumulation of exopolysaccharides and intracellular carbohydrates was observed. When nitrogen was added to the culture in the stationary phase, growth was resumed and the accumulation of exopolysaccharides was delayed. This indicated that nitrogen depletion caused cessation of growth, and stimulated exopolysaccharide accumulation. Exopolysaccharide accumulation was also stimulated when cells were either resuspended in medium lacking N or P, or when they were inoculated in medium with low concentrations of N or P. Growth was not immediately affected by low N or P concentrations. S depletion only resulted in exopolysaccharide accumulation when growth was affected. Si or Fe depletion did not stimulate exopolysaccharide accumulation, even when growth rates were lowered. Apparently, stimulation of exopolysaccharide accumulation is dependent on the type of nutrient depletion. Intracellular storage carbohydrates did not accumulate when cells were incubated at low N or P concentrations. Cells grown with ammonium as nitrogen source produced more carbohydrates (both extracellular and intracellular) than cells grown with nitrate as nitrogen source, indicating that both exopolysaccharides and intracellular carbohydrates accumulated as a result of overflow metabolism.

Temperature excludes N2-fixing heterocystous cyanobacteria in the tropical oceans

Whereas the non-heterocystous cyanobacteria Trichodesmium spp. are the dominant N2-fixing organisms in the tropical oceans, heterocystous species dominate N2 fixation in freshwater lakes and brackish environments such as the Baltic Sea. So far no satisfactory explanation for the absence of heterocystous cyanobacteria in the pelagic of the tropical oceans has been given, even though heterocysts would seem to represent an ideal strategy for protecting nitrogenase from being inactivated by O2, thereby enabling cyanobacteria to fix N2 and to perform photosynthesis simultaneously. Trichodesmium is capable of N2 fixation, apparently without needing to differentiate heterocysts. Here we show that differences in the temperature dependence of O2 flux, respiration and N2 fixation activity explain how Trichodesmium performs better than heterocystous species at higher temperatures. Our results also explain why Trichodesmium is not successful in temperate or cold seas. The absence of heterocystous cyanobacteria in the pelagic zone of temperate and cold seas, however, requires another explanation.

Colorful niches of phototrophic microorganisms shaped by vibrations of the water molecule.

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.

Biogenic Stabilization of Intertidal Sediments: The Importance of Extracellular Polymeric Substances Produced by Benthic Diatoms

The sediment-stabilizing effect of benthic diatoms was investigated in a laboratory setting. Axenic cultures of the benthic diatoms Nitzschia cf. brevissima and Cylindrotheca closterium were inoculated in Petri dishes containing sand and incubated under axenic conditions. By ensuring aseptic routines throughout the experiments, interference from other organisms occurring with diatoms in natural photothrophic biofilms was avoided. This allowed the examination of the role of benthic diatoms in sediment stabilization. Increases in the critical erosion shear stress of the sediment were observed in the presence of both diatom taxa relative to sterile sediment. However, N. cf. brevissima was more effective than C. closterium. Values of critical shear stress in the experimental system were in the same range as those observed in natural biofilms, which indicates that diatoms are important agents for biogenic stabilization. Extracellular carbohydrate contents in the microcosms were similar for both diatom species. However, in the presence of N cf. brevissima, extracellular carbohydrate correlated significantly to critical shear stress, explaining up to 80% of the variation, whereas this was not the case for C. closterium. Therefore, it was concluded that the quantity of extracellular polymeric substances (EPS) alone did not explain the biogenic stabilization. Observed adsorption of EPS to sediment particles depended on the relative amount of uronic acids in the exopolymers. Using fluorescently labeled lectins, confocal laser scanning microscopy showed that EPS secretion by N. cf. brevissima resulted in ordered three-dimensional matrix structures. It is suggested that the structuring of EPS plays an prominent role in the process of biostabilization, and that diatoms such as N. cf. brevissima are actively involved in producing the structure of EPS, whereas others such as C. closterium do not do so to the same extent.