Nutrient enrichment, grazer identity, and their effects on epiphytic algal assemblages: field experiments in subtropical turtlegrass Thalassia testudinum meadows

We tested the relative importance of top-down and bottom-up effects by experimentally evaluating the combined and separate effects of nutrient availability and grazer species composition on epiphyte communities and seagrass condition in Florida Bay. Although we succeeded in substantially enriching our experimental cylinders, as indicated by elevated nitrogen concentrations in epiphytes and seagrass leaves, we did not observe any major increases in epiphyte biomass or major loss of Thalassia testudinum by algal overgrowth. Additionally, we did not detect any strong grazer effects and found very few significant nutrient-grazer interactions. While this might suggest that there was no important differential response to nutrients by individual grazer species or by various combinations of grazers, our results were complicated by the lack of significant differences between control and grazer treatments, and as such, these results are best explained by the presence of unwanted amphipod grazers (mean = 471 ind. m–2) in the control cylinders. Our estimates of grazing rates and epiphyte productivities indicate that amphipods in the control cylinders could have lowered epiphyte biomass to the same level that the experimental grazers did, thus effectively transforming the control treatments into grazer treatments. If so, our experiments suggest that the effects of invertebrate grazing (and those of amphipods alone) were stronger than the effects of nutrient enrichment on epiphytic algae, and that it does not require a large density

A molecular and stable isotopic approach to investigate the importance of algal and detrital energy pathways in a freshwater marsh

The relative importance of algal and detrital energy pathways remains a central question in wetlands ecology. We used bulk stable isotope analysis and fatty acid composition to investigate the relative contributions of periphyton (algae) and floc (detritus) in a freshwater wetland with the goal of determining the inputs of these resource pools to lower trophic-level consumers. All animal samples revealed fatty acid markers indicative of both microbial (detrital) and algal origins, though the relative contributions varied among species. Vascular plant markers were in low abundance in most consumers. Detritivory is important for chironomids and amphipods, as demonstrated by the enhanced bacterial fatty acids present in both consumers, while algal resources, in the form of periphyton, likely support ephemeropteran larvae. Invertebrates such as amphipods and grass shrimp appear to be important resources for small omnivorous fish, while Poecilia latipinna appear to strongly use periphyton and Ephemeroptera larvae as food sources. Both P. latipinna and Lepomis spp. assimilated small amounts of vascular plant debris, possibly due to unintentional ingestion of floc while foraging for invertebrates and insect larvae. Physid snails, Haitia spp., were characterized by considerably different fatty acid compositions than other taxa examined, and likely play a unique role in Everglades’ food webs.

Contribution of lipophilic secondary metabolites to the toxicity of strains of freshwater cyanobacterial harmful algal blooms, identified using the zebrafish (Danio rerio) embryo as a model for vertebrate development

Cyanobacteria ("blue-green algae") are known to produce a diverse repertoire of biologically active secondary metabolites. When associated with so-called "harmful algal blooms", particularly in freshwater systems, a number of these metabolites have been associated—as "toxins", or commonly "cyanotoxins"—with human and animal health concerns. In addition to the known water-soluble toxins from these genera (i.e. microcystins, cylindrospermopsin, and saxitoxins), our studies have shown that there are metabolites within the lipophilic extracts of these strains that inhibit vertebrate development in zebrafish embryos. Following these studies, the zebrafish embryo model was implemented in the bioassay-guided purification of four isolates of cyanobacterial harmful algal blooms, namely Aphanizomenon, two isolates of Cylindrospermopsis, and Microcystis, in order to identify and chemically characterize the bioactive lipophilic metabolites in these isolates. ^ We have recently isolated a group of polymethoxy-1-alkenes (PMAs), as potential toxins, based on the bioactivity observed in the zebrafish embryos. Although PMAs have been previously isolated from diverse cyanobacteria, they have not previously been associated with relevant toxicity. These compounds seem to be widespread across the different genera of cyanobacteria, and, according to our studies, suggested to be derived from the polyketide biosynthetic pathway which is a common synthetic route for cyanobacterial and other algal toxins. Thus, it can be argued that these metabolites are perhaps important contributors to the toxicity of cyanobacterial blooms. In addition to the PMAs, a set of bioactive glycosidic carotenoids were also isolated because of their inhibition of zebrafish embryonic development. These pigmented organic molecules are found in many photosynthetic organisms, including cyanobacteria, and they have been largely associated with the prevention of photooxidative damage. This is the first indication of these compounds as toxic metabolites and the hypothesized mode of action is via their biotransformation to retinoids, some of which are known to be teratogenic. Additional fractions within all four isolates have been shown to contain other uncharacterized lipophilic toxic metabolites. This apparent repertoire of lipophilic compounds may contribute to the toxicity of these cyanobacterial harmful algal blooms, which were previously attributed primarily to the presence of the known water-soluble toxins.^

14C concentrations of algal and archaeal lipids and their associated sea surface temperature proxies in the Black Sea

Understanding the preservation and deposition history of organic molecules is crucial for the understanding of paleoenvironmental information contained in their abundance ratios such as Uk'37 and TEX86 used as proxies for sea surface temperature (SST). Based on their relatively high refractivity, alkenones and glycerol dialkyl glycerol tetraethers (GDGTs) can survive postdepositional processes like lateral transport, potentially causing inferred SSTs to be misleading. Likewise, selective preservation of alkenones and GDGTs may cause biases of the SST proxies themselves and can lead to decoupling of both proxy records. Here we report compound-specific radiocarbon data of marine biomarkers including alkenones, GDGTs, and low molecular weight (LMW) n-fatty acids from Black Sea sediments deposited under different redox regimes to evaluate the potentially differential preservation of both biomarker classes and its effect on the SST indices Uk'37 and TEX86 . The decadal D14C values of alkenones, GDGTs, and LMW n-fatty acids indicate similar preservation under oxic, suboxic, and anoxic redox regimes and no contribution of pre-aged compounds, e.g., by lateral supply. Moreover, similar 14C concentrations of crenarchaeol, alkenones, and LMW n-fatty acids imply that the thaumarchaeotal GDGTs preserved in these sediments are produced in the euphotic zone rather than in subsurface/thermocline waters. However, we observe biomarker-based SSTs that strongly deviate (deltaSST up to 8.4 °C) from in situ measured mean annual SSTs in the Black Sea. This is not due to redox-dependent differential biomarker preservation as implied by their D14C values and spatial SST pattern. Since contributions from different sources can largely be excluded, the deviation of the Uk'37 and TEX86 proxy-derived SSTs from in situ SSTs requires further study of phylogenetic and other yet unknown environmental controls on alkenone and GDGT lipid distributions in the Black Sea.

Data compilation on the biological response to ocean acidification: environmental and experimental context of data sets and related literature

The exponential growth of studies on the biological response to ocean acidification over the last few decades has generated a large amount of data. To facilitate data comparison, a data compilation hosted at the data publisher PANGAEA was initiated in 2008 and is updated on a regular basis (doi:10.1594/PANGAEA.149999). By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived. Here we present the developments of this data compilation five years since its first description by Nisumaa et al. (2010). Most of study sites from which data archived are still in the Northern Hemisphere and the number of archived data from studies from the Southern Hemisphere and polar oceans are still relatively low. Data from 60 studies that investigated the response of a mix of organisms or natural communities were all added after 2010, indicating a welcomed shift from the study of individual organisms to communities and ecosystems. The initial imbalance of considerably more data archived on calcification and primary production than on other processes has improved. There is also a clear tendency towards more data archived from multifactorial studies after 2010. For easier and more effective access to ocean acidification data, the ocean acidification community is strongly encouraged to contribute to the data archiving effort, and help develop standard vocabularies describing the variables and define best practices for archiving ocean acidification data.

Alteração do estado trófico durante um evento de seca prolongada e seus impactos na biomassa algal de um manancial tropical da região semiárida

The main consequence of eutrophication is an increase in algal biomass, mainly cyanobacterial blooms. The high evaporation and low precipitation, characteristics of semiarid regions, contribute to the nutrients availability increase in drought periods and consequent aggravation of eutrophic condition in reservoirs. Climate changes tend to intensify eutrophication symptoms, mostly in a semiarid region. Therefore, the aim of this study was to evaluate the impact of an extended drought in algal biomass in Parelhas’s Boqueirão, a mesotrophic reservoir located in a semiarid tropical region. The low volume was associated to water quality degradation and to the high nutrients concentrations and low water transparency. The increase in nutrients availability in the water column, consequence of reduced precipitation and low reservoir’s volume, provided the necessary resources for algal growth and allowed a change in trophic state in Boqueirão reservoir. This study showed how an extended drought decreases water quality. The effect of drought in Boqueirão was late detected due to the reservoir´s low initial nutrients concentration. The reservoir´s volume reduction increased the nutrient availability along with the algal biomass increase and the reservoir´s trophic state change of mesotrophic to eutrophic.

Radionuclides measured on 27 water bottle profiles during POLARSTERN cruise ANT-XXIV/3

As part of the GEOTRACES Polarstern expedition ANT XXIV/3 (ZERO and DRAKE) we have measured the vertical distribution of 234Th on sections through the Antarctic Circumpolar Current along the zero meridian and in Drake Passage and on an EW section through the Weddell Sea. Steady state export fluxes of 234Th from the upper 100m, derived from the depletion of 234Th with respect to its parent 238U, ranged from 621±105 dpm/m**2/d to 1773±90 dpm/m**2/d. This 234Th flux was converted into an export flux of organic carbon ranging from 3.1-13.2 mmolC/m**2/d (2.1-9.0 mmolC/m**2/d) using POC/234Th ratio of bulk (respectively >50 µm) suspended particles at the export depth (100 m). Non-steady state fluxes assuming zero flux under ice cover were up to 23% higher. In addition, particulate and dissolved 234Th were measured underway in high resolution in the surface water with a semi-automated procedure. Particulate 234Th in surface waters is inversely correlated with light transmission and pCO2 and positively with fluorescence and optical backscatter and is interpreted as a proxy for algal biomass. High resolution underway mapping of particulate and dissolved 234Th in surface water shows clearly where trace elements are absorbed by plankton and where they are exported to depth. Quantitative determination of the export flux requires the full 234Th profile since surface depletion and export flux become decoupled through changes in wind mixed layer depth and in contribution to export from subsurface layers. In a zone of very low algal abundance (54-58 °S at the zero meridian), confirmed by satellite Chl-a data, the lowest carbon export of the ACC was observed, allowing Fe and Mn to maintain their highest surface concentrations (Klunder et al., this issue, Middag et al., this issue). An ice-edge bloom that had developed in Dec/Jan in the zone 60-65 °S as studied during the previous leg (Strass et al., in prep) had caused a high export flux at 64.5 °S when we visited the area two months later (Feb/March). The ice-edge bloom had then shifted south to 65-69 °S evident from uptake of CO2 and dissolved Fe, Mn and 234Th, without causing export yet. In this way, the parallel analysis of 234Th can help to explain the scavenging behaviour of other trace elements.

Nitrate metabolism in the dinoflagellate Lingulodinium polyedrum

Les dinoflagellés sont des eucaryotes unicellulaires retrouvés dans la plupart des écosystèmes aquatiques du globe. Ces organismes amènent une contribution substantielle à la production primaire des océans, soit en tant que membre du phytoplancton, soit en tant que symbiontes des anthozoaires formant les récifs coralliens. Malheureusement, ce rôle écologique majeur est souvent négligé face à la capacité de certaines espèces de dinoflagellés à former des fleurs d'eau, parfois d'étendue et de durée spectaculaires. Ces floraisons d'algues, communément appelées "marées rouges", peuvent avoir de graves conséquences sur les écosystèmes côtiers, sur les industries de la pêche et du tourisme, ainsi que sur la santé humaine. Un des facteurs souvent corrélé avec la formation des fleurs d'eau est une augmentation dans la concentration de nutriments, notamment l’azote et le phosphore. Le nitrate est un des composants principaux retrouvés dans les eaux de ruissellement agricoles, mais également la forme d'azote bioaccessible la plus abondante dans les écosystèmes marins. Ainsi, l'agriculture humaine a contribué à magnifier significativement les problèmes associés aux marées rouges au niveau mondial. Cependant, la pollution ne peut pas expliquer à elle seule la formation et la persistance des fleurs d'eau, qui impliquent plusieurs facteurs biotiques et abiotiques. Il est particulièrement difficile d'évaluer l'importance relative qu'ont les ajouts de nitrate par rapport à ces autres facteurs, parce que le métabolisme du nitrate chez les dinoflagellés est largement méconnu. Le but principal de cette thèse vise à remédier à cette lacune. J'ai choisi Lingulodinium polyedrum comme modèle pour l'étude du métabolisme du nitrate, parce que ce dinoflagellé est facilement cultivable en laboratoire et qu'une étude transcriptomique a récemment fourni une liste de gènes pratiquement complète pour cette espèce. Il est également intéressant que certaines composantes moléculaires de la voie du nitrate chez cet organisme soient sous contrôle circadien. Ainsi, dans ce projet, j'ai utilisé des analyses physiologiques, biochimiques, transcriptomiques et bioinformatiques pour enrichir nos connaissances sur le métabolisme du nitrate des dinoflagellés et nous permettre de mieux apprécier le rôle de l'horloge circadienne dans la régulation de cette importante voie métabolique primaire. Je me suis tout d'abord penché sur les cas particuliers où des floraisons de dinoflagellés sont observées dans des conditions de carence en azote. Cette idée peut sembler contreintuitive, parce que l'ajout de nitrate plutôt que son épuisement dans le milieu est généralement associé aux floraisons d'algues. Cependant, j’ai découvert que lorsque du nitrate était ajouté à des cultures initialement carencées ou enrichies en azote, celles qui s'étaient acclimatées au stress d'azote arrivaient à survivre près de deux mois à haute densité cellulaire, alors que les cellules qui n'étaient pas acclimatées mourraient après deux semaines. En condition de carence d'azote sévère, les cellules arrivaient à survivre un peu plus de deux semaines et ce, en arrêtant leur cycle cellulaire et en diminuant leur activité photosynthétique. L’incapacité pour ces cellules carencées à synthétiser de nouveaux acides aminés dans un contexte où la photosynthèse était toujours active a mené à l’accumulation de carbone réduit sous forme de granules d’amidon et corps lipidiques. Curieusement, ces deux réserves de carbone se trouvaient à des pôles opposés de la cellule, suggérant un rôle fonctionnel à cette polarisation. La deuxième contribution de ma thèse fut d’identifier et de caractériser les premiers transporteurs de nitrate chez les dinoflagellés. J'ai découvert que Lingulodinium ne possédait que très peu de transporteurs comparativement à ce qui est observé chez les plantes et j'ai suggéré que seuls les membres de la famille des transporteurs de nitrate de haute affinité 2 (NRT2) étaient réellement impliqués dans le transport du nitrate. Le principal transporteur chez Lingulodinium était exprimé constitutivement, suggérant que l’acquisition du nitrate chez ce dinoflagellé se fondait majoritairement sur un système constitutif plutôt qu’inductible. Enfin, j'ai démontré que l'acquisition du nitrate chez Lingulodinium était régulée par la lumière et non par l'horloge circadienne, tel qu'il avait été proposé dans une étude antérieure. Finalement, j’ai utilisé une approche RNA-seq pour vérifier si certains transcrits de composantes impliquées dans le métabolisme du nitrate de Lingulodinium étaient sous contrôle circadien. Non seulement ai-je découvert qu’il n’y avait aucune variation journalière dans les niveaux des transcrits impliqués dans le métabolisme du nitrate, j’ai aussi constaté qu’il n’y avait aucune variation journalière pour n’importe quel ARN du transcriptome de Lingulodinium. Cette découverte a démontré que l’horloge de ce dinoflagellé n'avait pas besoin de transcription rythmique pour générer des rythmes physiologiques comme observé chez les autres eukaryotes.

Algal Calcification and Silicification

The algae represent major producers of calcium carbonate and silica among the world's biota. Calcification involves the precipitation of CaCO3 from Ca2+ and CO32− ions. Algal calcification by coccolithophores may account for up to half of global oceanic CaCO3 production. Silicification, the transformation of silicic acid into skeletal material, occurs in a few algal groups. The abundant diatoms represent the major silicifiers, playing a key role in marine silica cycling. Fossilised diatomaceous deposits have long been exploited for building and filling materials. Biomineralisation of calcium and silicon require homeostatic ion controls that are well characterised for Ca2+ and H+ in coccolithophores. Calcification occurs in an alkalinised vesicle, while silicification requires an acidic pH. Research on silicification remains focused upon cell wall development. Initiation and development of structures that are mineralised intracellularly requires initiation and regulation by organic components within the vesicles. Low-temperature, low-pressure biogenic formation of silica and calcite has potential for biotechnological application in novel industrial processes.

Algal Calcification and Silicification

The algae represent major producers of calcium carbonate and silica among the world's biota. Calcification involves the precipitation of CaCO3 from Ca2+ and CO32− ions. Algal calcification by coccolithophores may account for up to half of global oceanic CaCO3 production. Silicification, the transformation of silicic acid into skeletal material, occurs in a few algal groups. The abundant diatoms represent the major silicifiers, playing a key role in marine silica cycling. Fossilised diatomaceous deposits have long been exploited for building and filling materials. Biomineralisation of calcium and silicon require homeostatic ion controls that are well characterised for Ca2+ and H+ in coccolithophores. Calcification occurs in an alkalinised vesicle, while silicification requires an acidic pH. Research on silicification remains focused upon cell wall development. Initiation and development of structures that are mineralised intracellularly requires initiation and regulation by organic components within the vesicles. Low-temperature, low-pressure biogenic formation of silica and calcite has potential for biotechnological application in novel industrial processes.

Interannual and (multi-)decadal variability in the sedimentary BIT index of Lake Challa, East Africa, over the past 2200 years: assessment of the precipitation proxy

The branched vs. isoprenoid tetraether (BIT) index is based on the relative abundance of branched tetraether lipids (brGDGTs) and the isoprenoidal GDGT crenarchaeol. In Lake Challa sediments the BIT index has been applied as a proxy for local monsoon precipitation on the assumption that the primary source of brGDGTs is soil washed in from the lake's catchment. Since then, microbial production within the water column has been identified as the primary source of brGDGTs in Lake Challa sediments, meaning that either an alternative mechanism links BIT index variation with rainfall or that the proxy's application must be reconsidered. We investigated GDGT concentrations and BIT index variation in Lake Challa sediments at a decadal resolution over the past 2200 years, in combination with GDGT time-series data from 45 monthly sediment-trap samples and a chronosequence of profundal surface sediments.

Our 2200-year geochemical record reveals high-frequency variability in GDGT concentrations, and therefore in the BIT index, superimposed on distinct lower-frequency fluctuations at multi-decadal to century timescales. These changes in BIT index are correlated with changes in the concentration of crenarchaeol but not with those of the brGDGTs. A clue for understanding the indirect link between rainfall and crenarchaeol concentration (and thus thaumarchaeotal abundance) was provided by the observation that surface sediments collected in January 2010 show a distinct shift in GDGT composition relative to sediments collected in August 2007. This shift is associated with increased bulk flux of settling mineral particles with high Ti / Al ratios during March–April 2008, reflecting an event of unusually high detrital input to Lake Challa concurrent with intense precipitation at the onset of the principal rain season that year. Although brGDGT distributions in the settling material are initially unaffected, this soil-erosion event is succeeded by a massive dry-season diatom bloom in July–September 2008 and a concurrent increase in the flux of GDGT-0. Complete absence of crenarchaeol in settling particles during the austral summer following this bloom indicates that no Thaumarchaeota bloom developed at that time. We suggest that increased nutrient availability, derived from the eroded soil washed into the lake, caused the massive bloom of diatoms and that the higher concentrations of ammonium (formed from breakdown of this algal matter) resulted in a replacement of nitrifying Thaumarchaeota, which in typical years prosper during the austral summer, by nitrifying bacteria. The decomposing dead diatoms passing through the suboxic zone of the water column probably also formed a substrate for GDGT-0-producing archaea. Hence, through a cascade of events, intensive rainfall affects thaumarchaeotal abundance, resulting in high BIT index values.

Decade-scale BIT index fluctuations in Lake Challa sediments exactly match the timing of three known episodes of prolonged regional drought within the past 250 years. Additionally, the principal trends of inferred rainfall variability over the past two millennia are consistent with the hydroclimatic history of equatorial East Africa, as has been documented from other (but less well dated) regional lake records. We therefore propose that variation in GDGT production originating from the episodic recurrence of strong soil-erosion events, when integrated over (multi-)decadal and longer timescales, generates a stable positive relationship between the sedimentary BIT index and monsoon rainfall at Lake Challa. Application of this paleoprecipitation proxy at other sites requires ascertaining the local processes which affect the productivity of crenarchaeol by Thaumarchaeota and brGDGTs.

A Study of Privacy Preserving Queries with Bloom Filters

This thesis focuses on the private membership test (PMT) problem and presents three single server protocols to resolve this problem. In the presented solutions, a client can perform an inclusion test for some record x in a server's database, without revealing his record. Moreover after executing the protocols, the contents of server's database remain secret. In each of these solutions, a different cryptographic protocol is utilized to construct a privacy preserving variant of Bloom filter. The three suggested solutions are slightly different from each other, from privacy perspective and also from complexity point of view. Therefore, their use cases are different and it is impossible to choose one that is clearly the best between all three. We present the software developments of the three protocols by utilizing various pseudocodes. The performance of our implementation is measured based on a real case scenario. This thesis is a spin-off from the Academy of Finland research project "Cloud Security Services".