Charles Vidoudez

Comparative metabolomics of the diatom Skeletonema marinoi in different growth phases

We introduce a rigorously validated protocol based on extraction, derivatisation and GC/MS for the analysis of diatom metabolomes. Using this methodology we characterised general patterns of the metabolism of the diatom Skeletonema marinoi during different growth phases. Canonical analysis of principal coordinate revealed clearly that the intracellular metabolites differ between exponential, stationary and declining phase. In addition, diurnal variation during the exponential phase was observed. A detailed analysis of the metabolic changes is presented and discussed in the context of previous physiological studies of diatoms. The observed variability in metabolites has a significant consequence for further physiological and ecological studies. Investigations have to take into account that diatom metabolism is a highly dynamic process and that food quality, chemical defence and also the production of signal molecules might be dependent on different growth phases or diurnal variations. The introduced protocol is in general suitable for the monitoring of microalgae and has also the potential to be applied to complex plankton communities.

Electron uptake by iron-oxidizing phototrophic bacteria

Oxidation-reduction reactions underlie energy generation in nearly all life forms. Although most organisms use soluble oxidants and reductants, some microbes can access solid-phase materials as electron-acceptors or -donors via extracellular electron transfer. Many studies have focused on the reduction of solid-phase oxidants. Far less is known about electron uptake via microbial extracellular electron transfer, and almost nothing is known about the associated mechanisms. Here we show that the iron-oxidizing photoautotroph Rhodopseudomonas palustris TIE-1 accepts electrons from a poised electrode, with carbon dioxide as the sole carbon source/electron acceptor. Both electron uptake and ruBisCo form I expression are stimulated by light. Electron uptake also occurs in the dark, uncoupled from photosynthesis. Notably, the pioABC operon, which encodes a protein system essential for photoautotrophic growth by ferrous iron oxidation, influences electron uptake. These data reveal a previously unknown metabolic versatility of photoferrotrophs to use extracellular electron transfer for electron uptake.

Quantification of Dissolved and Particulate Polyunsaturated Aldehydes in the Adriatic Sea

Polyunsaturated aldehydes (PUA) are supposed to play critical roles in chemically-mediated plankton interactions. Laboratory studies suggest that they act as mediators of chemical defense and chemical communication. PUA are oxylipins containing an α,β,γ,δ–unsaturated aldehyde structure element and are mainly found in diatoms. We present here a detailed surface mapping of PUA during a spring bloom of the diatom Skeletonema marinoi in the Adriatic Sea. We monitored dissolved PUA, as well as particulate PUA, which are produced by phytoplankton after cell disintegration. Our survey revealed a patchy distribution of PUA and shows that at most stations S. marinoi is the major contributor to the overall PUA. Our data also suggest that lysis of a diatom bloom can contribute significantly to the dissolved PUA concentrations and that other producers, which are smaller in cell size compared to diatoms, have to be taken into account as well if the total PUA content of marine samples is considered. The analyses of samples collected in deeper water suggests that diatom contribution to PUA decreases with depth, while smaller-sized unidentified organisms take place as dominant contributors to the PUA concentrations.

Characterizing the distribution and rates of microbial sulfate reduction at Middle Valley hydrothermal vents

Few studies have directly measured sulfate reduction at hydrothermal vents, and relatively little is known about how environmental or ecological factors influence rates of sulfate reduction in vent environments. A better understanding of microbially mediated sulfate reduction in hydrothermal vent ecosystems may be achieved by integrating ecological and geochemical data with metabolic rate measurements. Here we present rates of microbially mediated sulfate reduction from three distinct hydrothermal vents in the Middle Valley vent field along the Juan de Fuca Ridge, as well as assessments of bacterial and archaeal diversity, estimates of total biomass and the abundance of functional genes related to sulfate reduction, and in situ geochemistry. Maximum rates of sulfate reduction occurred at 90 °C in all three deposits. Pyrosequencing and functional gene abundance data revealed differences in both biomass and community composition among sites, including differences in the abundance of known sulfate-reducing bacteria. The abundance of sequences for Thermodesulfovibro-like organisms and higher sulfate reduction rates at elevated temperatures suggests that Thermodesulfovibro-like organisms may have a role in sulfate reduction in warmer environments. The rates of sulfate reduction presented here suggest that—within anaerobic niches of hydrothermal deposits—heterotrophic sulfate reduction may be quite common and might contribute substantially to secondary productivity, underscoring the potential role of this process in both sulfur and carbon cycling at vents.

High plasticity in the production of diatom-derived polyunsaturated aldehydes under nutrient limitation: physiological and ecological implications.

Diatoms have evolved a silicified cell wall that provides an efficient barrier against herbivores. These microalgae also produce chemical compounds such as polyunsaturated aldehydes (PUAs) that can potentially impair recruitment and cause malformations in the offspring of such grazers. We measured silica content as an indication of cell wall thickness, organic nutrient cell quotas, PUAs and polyunsaturated fatty acid cell content in Skeletonema marinoi grown under N-, P- and Si-limitation in continuous cultures. A 7.5 fold increase in PUA production was observed (27.5 fmol cell(-1)) in Si-limited cells with respect to the controls, while Si content decreased by 50%. PUA production decreased in nitrogen-limited cells to 0.14 fmol cell(-1) and increased 3 times in phosphorus-limited cells (7.53 fmol cell(-1)), while silica content increased by 20% in both cases. The substrate to product ratio suggested that production of the PUAs heptadienal and octadienal was limited by the amount of substrate under P- and Si-limitation, and by enzyme activity under N-limitation. Octatrienal production was likely limited by enzyme activity in all growth conditions. The high PUA levels produced under Si-limitation, when cells have a thinner cell wall, suggests a compensatory alternation of mechanical and chemical defense mechanisms.

Dynamics of Dissolved and Particulate Polyunsaturated Aldehydes in Mesocosms Inoculated with Different Densities of the Diatom Skeletonema marinoi

A survey of the production of polyunsaturated aldehydes (PUA) of manipulated plankton communities is presented here. PUA are phytoplankton-derived metabolites that are proposed to play an important role in chemically mediated plankton interactions. Blooms of different intensities of the diatom Skeletonema marinoi were generated in eight mesocosms filled with water from the surrounding fjord by adding different amounts of a starting culture and nutrients. This set-up allowed us to follow PUA production of the plankton community over the entire induced bloom development, and to compare it with the natural levels of PUA. We found that S. marinoi is a major source for the particulate PUA 2,4-heptadienal and 2,4-octadienal (defined as PUA released upon wounding of the diatom cells) during the entire bloom development. Just before, and during, the decline of the induced diatom blooms, these PUA were also detected in up to 1 nM concentrations dissolved in the water. In addition, we detected high levels of the PUA 2,4-decadienal that was not produced by the diatom S. marinoi. Particulate decadienal correlated well with the cell counts of the prymnesiophyte Phaeocystis sp. that also developed in the fertilized mesocosms. Particulate decadienal levels were often even higher than those of diatom-derived PUA, indicating that PUA sources other than diatoms should be considered when it comes to the evaluation of the impact of these metabolites.

Phytoplankton cell lysis associated with polyunsaturated aldehyde release in the Northern Adriatic Sea.

Diatoms are able to react to biotic and abiotic stress, such as competition, predation and unfavorable growth conditions, by producing bioactive compounds including polyunsaturated aldehydes (PUAs). PUAs have been shown to act against grazers and either enhance or inhibit the growth of different phytoplankton and bacteria both in culture and in the field. Presence of nanomolar concentrations of dissolved PUAs in seawater has been reported in the North Adriatic Sea (Mediterranean), suggesting that these compounds are released in seawater following diatom cell lysis. However, the origin of the PUAs and their effects on natural phytoplankton assemblages remain unclear. Here we present data from four oceanographic cruises that took place during diatom blooms in the northern Adriatic Sea where concentrations of particulate and dissolved PUAs were monitored along with phytoplankton cell lysis. Cell lysis was positively correlated with both concentrations of particulate and dissolved PUAs (R = 0.69 and R = 0.77, respectively), supporting the hypothesis that these compounds are released by cell lysis. However, the highest concentration of dissolved PUAs (2.53 nM) was measured when cell lysis was high (0.24 d−1) but no known PUA-producing diatoms were detected, suggesting either that other organisms can produce PUAs or that PUA-producing enzymes retain activity extracellularly after diatom cells have lysed. Although in situ concentrations of dissolved PUAs were one to three orders of magnitude lower than those typically used in laboratory culture experiments, we argue that concentrations produced in the field could induce similar effects to those observed in culture and therefore may help shape plankton community composition and function in the oceans.

Characterizing the distribution of methane sources and cycling in the deep sea via in situ stable isotope analysis.

The capacity to make in situ geo-referenced measurements of methane concentration and stable isotopic composition (δ(13)C(CH4)) would greatly improve our understanding of the distribution and type of methane sources in the environment, allow refined determination of the extent to which microbial production and consumption contributes to methane cycling, and enable the testing of hypotheses about the sensitivity of methane cycling to changes in environmental conditions. In particular, characterizing biogeochemical methane cycling dynamics in the deep ocean is hampered by a number of challenges, especially in environments where high methane concentrations preclude intact recovery of undisturbed samples. To that end, we have developed an in situ analyzer capable of δ(13)C(CH4) measurements in the deep ocean. Here we present data from laboratory and field studies in which we characterize the instruments analytical capabilities and performance and provide the first in situ stable isotope based characterization of the influence of anaerobic methane oxidation on methane flux from seep sediments. These data illustrate how in situ measurements can permit finer-scale analyses of variations in AOM activity, and facilitate advances in using δ(13)C(CH4) and other isotopic systems to interrogate biogeochemical cycles in the deep sea and other remote or challenging environments.

Strain-related physiological and behavioral effects of Skeletonema marinoi on three common planktonic copepods

Three strains of the chain-forming diatom Skeletonema marinoi, differing in their production of polyunsaturated aldehydes (PUA) and nutritional food components, were used in experiments on feeding, egg production, hatching success, pellet production, and behavior of three common planktonic copepods: Acartia tonsa, Pseudocalanus elongatus, and Temora longicornis. The three different diatom strains (9B, 1G, and 7J) induced widely different effects on Acartia tonsa physiology, and the 9B strain induced different effects for the three copepods. In contrast, different strains induced no or small alterations in the distribution, swimming behavior, and turning frequency of the copepods. 22:6(n-3) fatty acid (DHA) and sterol content of the diet typically showed a positive effect on either egg production (A. tonsa) or hatching success (P. elongatus), while other measured compounds (PUA, other long-chain polyunsaturated fatty acids) of the algae had no obvious effects. Our results demonstrate that differences between strains of a given diatom species can generate effects on copepod physiology, which are as large as those induced by different algae species or groups. This emphasizes the need to identify the specific characteristics of local diatoms together with the interacting effects of different mineral, biochemical, and toxic compounds and their potential implications on different copepod species.

Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents

At deep-sea hydrothermal vents, primary production is carried out by chemolithoautotrophic microorganisms, with the oxidation of reduced sulfur compounds being a major driver for microbial carbon fixation. Dense and highly diverse assemblies of sulfur-oxidizing bacteria (SOB) are observed, yet the principles of niche differentiation between the different SOB across geochemical gradients remain poorly understood. In this study niche differentiation of the key SOB was addressed by extensive sampling of active sulfidic vents at six different hydrothermal venting sites in the Manus Basin, off Papua New Guinea. We subjected 33 diffuse fluid and water column samples and 23 samples from surfaces of chimneys, rocks and fauna to a combined analysis of 16S rRNA gene sequences, metagenomes and real-time in situ measured geochemical parameters. We found Sulfurovum Epsilonproteobacteria mainly attached to surfaces exposed to diffuse venting, while the SUP05-clade dominated the bacterioplankton in highly diluted mixtures of vent fluids and seawater. We propose that the high diversity within Sulfurimonas- and Sulfurovum-related Epsilonproteobacteria observed in this study derives from the high variation of environmental parameters such as oxygen and sulfide concentrations across small spatial and temporal scales.