Mastogloia smithii var lacustris Grun.: A Structural Engineer of Calcareous Mats in Karstic Subtropical Wetlands

Mastogloia smithii var. lacustris Grun. is the dominant diatom in periphyton mats of the calcareous, freshwater to brackish wetlands of Caribbean coasts. Despite oligotrophy, frequent desiccation, high irradiance and temperatures, and occasional fire, periphyton communities in these wetlands can produce over 2000 g m-2 of organic biomass, prompting studies that examine stress resistance and maintenance of algal mats under extreme conditions. The diatom flora inhabiting periphyton mats from over 500 sites in the Florida Everglades and similar wetlands in Belize, Jamaica and Mexico was examined, and M. smithii var. lacustris was a persistent component, present in 97% of samples and comprising up to 80% of a diverse diatom assemblage. Valves at various stages of division were observed encased in extracellular polysaccharide that exceeded the cell volume; SEM observations confirm issuance from mantle pores resulting in suspension of the cell in a matrix dominated by cyanobacterial filaments. Using corresponding biophysical data from the collection sites, we define the optima for M. smithii var. lacustris along salinity, pH, phosphorus, and water depth gradients. Experiments revealed a collapse of M. smithii var. lacustris populations in the presence of above-ambient phosphorus concentrations and a rapid resurgence upon reflooding of desiccated mats. This widespread diatom taxon appears to play a critical role similar to that of cyanobacteria in microbial mats, and its disappearance in the presence of enrichment threatens biodiversity and the natural function in these systems that are increasingly influenced by urbanization

Black band disease: Elucidating origins and disease mechanisms

Coral diseases were unknown in the scientific community fifty years ago. Since the discovery of a coral disease in 1965, there has been an exponential increase in the number of known coral diseases, as the abundance, prevalence, distribution, and number of host species affected has also significantly increased. Coral diseases are recognized as contributing significantly to the dramatic losses of coral cover on a global basis, particularly in the Caribbean. The apparent sudden emergence of coral diseases suggests that they may be a symptom of an overall trend associated with changing environmental conditions. However, not much evidence has been gathered to address this question. The following studies were designed to build a comprehensive argument to support this hypothesis for one important coral disease—black band disease (BBD). A meta-analysis of clone libraries identifying the microbial communities associated with BBD reveal important information including that a single cyanobacterial operational taxonomic unit (OTU) was by far the most prevalent OTU in diseased samples, and that the alphaproteobacteria, which include some of the most common bacteria in marine waters, were the most diversely represented. The analysis also showed that samples exhibited regional similarities. An fine and ultrastructural characterization of the disease revealed that the cyanobacteria are prolific borers through the coral skeleton, and that the cyanobacteria penetrate coral tissue, leading to their presence ahead of the main migrating disease band. It was further found that apparently healthy corals exposed to toxins found in BBD, exhibited similar tissue degradation to those infected with BBD. Comparing the disease progression to biofilm formation, it was determined that scouting cyanobacteria may contribute to the migration of the disease through progressive biofilm development over intact coral tissue. Together, these studies provide significant evidence for the hypothesis that BBD is an opportunistic disease, caused by common environmental bacteria, facilitated by the changing environmental conditions associated with climate change.

Florida Bay: Water quality status and trends, historic and emerging algal bloom problems

Florida Bay is a unique subtropical estuary that while historically oligotrophic, has been subjected to both natural and anthropogenic stressors, including hurricanes, coastal eutrophication and other impacts. These stressors have resulted in degradation of water quality in the past several decades, most evidenced by reoccurring blooms of the picocyanobacterium Synechococcus spp. Major nutrient inputs consist of freshwater flows to the eastern region from runoff and regulated canal releases, inputs from the Everglades to the central region via Taylor Slough, exchanges with the Gulf of Mexico, which include intermittent Shark River inputs to the western region, stormwater and wastewater from the Florida Keys, and atmospheric deposition. These nutrient inputs have resulted in a transition from strong phosphorus (P) limitation of phytoplankton in the eastern bay to nitrogen (N) limitation in the western bay. Large blooms of Synechococcus were most pronounced in the central bay region, in the area of transition between P and N limitation, in the mid-1990s. Although non-toxic, these blooms, which have continued intermittently through the early 2000s, resulted in significant sea-grass and benthic organism mortalities. A new suite of stressors in 2005, including the passages of Hurricanes Katrina, Rita, and Wilma, additional canal releases, and the initiation of road construction to widen the main roadway leading to the Keys, were correlated with a large Synechococcus bloom in the previously clear, strongly P- limited, northeastern region of the bay. Sustained for 3 years, this bloom was accompanied by a shift from P limitation to N limitation during its course. Nutrient bioassay experiments suggest that this bloom persisted due to the ability of Synechococcus to access organic N and P sources, microbial and geochemical cycling of organic and inorganic nutrients in the water column and between the water column and sediments (both suspended particles and benthos), and decreased grazing by benthic fauna due to their die-off.

Application of excitation emission matrix fluorescence monitoring in the assessment of spatial and seasonal drivers of dissolved organic matter composition: Sources and physical disturbance controls

The environmental dynamics of dissolved organic matter (DOM) were characterized for a shallow, subtropical, seagrass-dominated estuarine bay, namely Florida Bay, USA. Large spatial and seasonal variations in DOM quantity and quality were assessed using dissolved organic C (DOC) measurements and spectrophotometric properties including excitation emission matrix (EEM) fluorescence with parallel factor analysis (PARAFAC). Surface water samples were collected monthly for 2 years across the bay. DOM characteristics were statistically different across the bay, and the bay was spatially characterized into four basins based on chemical characteristics of DOM as determined by EEM-PARAFAC. Differences between zones were explained based on hydrology, geomorphology, and primary productivity of the local seagrass community. In addition, potential disturbance effects from a very active hurricane season were identified. Although the overall seasonal patterns of DOM variations were not significantly affected on a bay-wide scale by this disturbance, enhanced freshwater delivery and associated P and DOM inputs (both quantity and quality) were suggested as potential drivers for the appearance of algal blooms in high impact areas. The application of EEM-PARAFAC proved to be ideally suited for studies requiring high sample throughput methods to assess spatial and temporal ecological drivers and to determine disturbance-induced impacts in aquatic ecosystems.

Antibacterial Activity of Extracellular Products from Cyanobacteria.

Cyanobacteria are photosynthetic prokaryotes that can be found in freshwater and marine environments as well as in soil. These organisms produce a variety of different biologically active compounds exhibiting anti-bacterial, anti-fungal and anti-cancer properties among others. In this study, cyanobacterial isolates were screened for their ability to produce extracellular antibacterial products. Cyanobacteria were isolated from fresh water and soil samples collected in the Pembroke Pines, FL area. Twenty- seven strains of cyanobacteria were isolated belonging to the following genera: Limnothrix, Nostoc, Fischerella, Anabaena, Pseudoanabaena, Lyngbya, Leptolyngbya, Tychonema, and Calothrix. Individual strains were grown in liquid culture in laboratory conditions. Following 14-day cultivation, the culture liquid was filtered and tested for activity against the following bacteria: Escherichia coli, Bacillus megatarium, Staphylococcus aureus, and Micrococcus luteus. Among all genera of cyanobacterial strains tested, Fischerella exhibited the greatest inhibitory activity. An attempt was made to isolate the active compound from the culture liquid of the active strains. Lipophilic extracts from culture liquid were obtained from three selected Fischerella strains. The extracts proved to have varying levels of activity against the tested bacteria. Inhibitory activity from all three Fischerella strains was detected against B. megatarium and M luteus. The only strain that was active against S. aureus was Fischerella sp. 114-12 while none of the extracts showed activity against E. coli. This kind of screening has potential pharmaceutical and agricultural benefits, including possible discovery of novel antibiotics.

Mosquito larvicides from cyanobacteria

Cyanobacteria (blue-green algae) produce a diverse array of toxic or otherwise bioactive metabolites. These allelochemicals may also play a role in defense against potential predators and grazers, particularly aquatic invertebrates and their larvae, including mosquitoes. Compounds derived from cyanobacteria collected from the Florida Everglades and other Florida waterways were investigated as insecticides against the mosquito Aedes aegypti, a vector of dengue and yellow fever. Screening of cyanobacterial biomass revealed several strains that exhibited mosquito larvicidal activity. Guided via bioassay guided fractionation, a non-polar compound from Leptolyngbya sp. 21-9-3 was found to be the most active component. Characterization revealed the prospective compound to be a monounsaturated fatty acid with the molecular formula C16H30O2. This is the first evidence of mosquito larvicidal activity for this particular fatty acid. With larvicidal becoming more prevalent, fatty acids should be explored for future mosquito control strategies.^

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.

Sediment, water and biomass characteristics along gradients in Kongsfjorden, Svalbard

In contrast to numerous studies on the biomass of marine microphytobenthos from temperate coastal ecosystems, little is known from polar regions. Therefore, microphytobenthos biomass was measured at several coastal sites in Arctic Kongsfjorden (Spitsbergen) during the polar summer (June-August 2006). On sandy sediments, chla varied between 8 and 200 mg/m**2 and was related to water depth, current/wave exposure and geographical location. Biomass was rather independent of abiotic parameters such as sediment properties, salinity, temperature or light availability. At three stations, sediments at water depths of 3-4, 10, 15, 20 and 30 m were investigated to evaluate the effect of light availability on microalgae. Significant differences in distribution patterns of biomass in relation to deeper waters >10 m were found. The productive periods were not as distinct as phytoplankton blooms. Only at 3-4 m water depth at all three stations were two- to threefold increases of biomass measured during the investigation period. Hydrodynamic conditions seemed to be the driving force for differences in sediment colonisation by benthic microalgae. In spite of the extreme Arctic environmental conditions for algal growth, microphytobenthos biomass was comparable to marine temperate waters.

(Table 2) Radiocarbon ages of selected southern Baja California sediment cores

Piston, gravity, and multicores as well as hydrographic data were collected along the Pacific margin of Baja California to reconstruct past variations in the intensity of the oxygen-minimum zone (OMZ). Gravity cores collected from within the OMZ north of 24°N did not contain laminated surface sediments even though bottom water oxygen (BWO) concentrations were close to 5 µmol/kg. However, many of the cores collected south of 24°N did contain millimeter- to centimeter-scale, brown to black laminations in Holocene and older sediments but not in sediments deposited during the Last Glacial Maximum. In addition to the dark laminations, Holocene sediments in Soledad Basin, silled at 290 m, also contain white coccolith laminae that probably represent individual blooms. Two open margin cores from 430 and 700 m depth that were selected for detailed radiocarbon dating show distinct transitions from bioturbated glacial sediment to laminated Holocene sediment occurring at 12.9 and 11.5 ka, respectively. The transition is delayed and more gradual (11.3-10.0 ka) in another dated core from Soledad Basin. The observations indicate that bottom-water oxygen concentrations dropped below a threshold for the preservation of laminations at different times or that a synchronous hydrographic change left an asynchronous sedimentary imprint due to local factors. With the caveat that laminated sections should therefore not be correlated without independent age control, the pattern of older sequences of laminations along the North American western margin reported by this and previous studies suggests that multiple patterns of regional productivity and ventilation prevailed over the past 60 kyr.

Shell flux and oxygen isotope data of North Atlantic foraminifera

We present an almost 3 year long time series of shell fluxes and oxygen isotopes of left-coiling Neogloboquadrina pachyderma and Turborotalita quinqueloba from sediment traps moored in the deep central Irminger Sea. We determined their response to the seasonal change from a deeply mixed water column with occasional deep convection in winter to a thermally stratified water column with a surface mixed layer (SML) of around 50 m in summer. Both species display very low fluxes during winter with a remnant summer population holding out until replaced by a vital population that seeds the subsequent blooms. This annual population overturning is marked by a 0.7 per mill increase in d18O in both species. The shell flux of N. pachyderma peaks during the spring bloom and in late summer, when stratification is close to its minimum and maximum, respectively. Both export periods contribute about equally and account for >95% of the total annual flux. Shell fluxes of T. quinqueloba show only a single broad pulse in summer, thus following the seasonal stratification cycle. The d18O of N. pachyderma reflects temperatures just below the base of the seasonal SML without offset from isotopic equilibrium. The d18O pattern of T. quinqueloba shows a nearly identical amplitude and correlates highly with the d18O of N. pachyderma. Therefore T. quinqueloba also reflects temperature near the base of the SML but with a positive offset from isotopic equilibrium. These offsets contrast with observations elsewhere and suggest a variable offset from equilibrium calcification for both species. In the Irminger Sea the species consistently show a contrast in their flux timings. Their flux-weighted delta d18O will thus dominantly be determined by seasonal temperature differences at the base of the SML rather than by differences in their depth habitat. Consequently, their sedimentary delta d18O may be used to infer the seasonal contrast in temperature at the base of the SML.

High-Resolution In Situ Oxygen-Argon Studies of Surface Biological and Physical Processes in the Polar Oceans

The Arctic Ocean and Western Antarctic Peninsula (WAP) are the fastest warming regions on the planet and are undergoing rapid climate and ecosystem changes. Until we can fully resolve the coupling between biological and physical processes we cannot predict how warming will influence carbon cycling and ecosystem function and structure in these sensitive and climactically important regions. My dissertation centers on the use of high-resolution measurements of surface dissolved gases, primarily O2 and Ar, as tracers or physical and biological functioning that we measure underway using an optode and Equilibrator Inlet Mass Spectrometry (EIMS). Total O2 measurements are common throughout the historical and autonomous record but are influenced by biological (net metabolic balance) and physical (temperature, salinity, pressure changes, ice melt/freeze, mixing, bubbles and diffusive gas exchange) processes. We use Ar, an inert gas with similar solubility properties to O2, to devolve distinct records of biological (O2/Ar) and physical (Ar) oxygen. These high-resolution measurements that expose intersystem coupling and submesoscale variability were central to studies in the Arctic Ocean, WAP and open Southern Ocean that make up this dissertation.

Key findings of this work include the documentation of under ice and ice-edge blooms and basin scale net sea ice freeze/melt processes in the Arctic Ocean. In the WAP O2 and pCO2 are both biologically driven and net community production (NCP) variability is controlled by Fe and light availability tied to glacial and sea ice meltwater input. Further, we present a feasibility study that shows the ability to use modeled Ar to derive NCP from total O2 records. This approach has the potential to unlock critical carbon flux estimates from historical and autonomous O2 measurements in the global oceans.

Nvidia, matrox, paper? - Undergraduate game design tools in the humanities and social sciences

Eschewing costly high-tech approaches, this paper looks at the experience of using low-tech approaches to game design assignments as problem based learning and assessment tool over a number of years in undergraduate teaching. General game design concepts are discussed, along with learning outcomes and assessment rubrics in line with Blooms Taxonomy based on evidence from students who had no prior experience of serious game play or design. Approaches to creating game design based assessments are offered.

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.

Quantitative Analysis and Determination of Microcystin in water by Capillary Electrophoresis Mass Spectrometry

The presence of harmful algal blooms (HAB) is a growing concern in aquatic environments. Among HAB organisms, cyanobacteria are of special concern because they have been reported worldwide to cause environmental and human health problem through contamination of drinking water. Although several analytical approaches have been applied to monitoring cyanobacteria toxins, conventional methods are costly and time-consuming so that analyses take weeks for field sampling and subsequent lab analysis. Capillary electrophoresis (CE) becomes a particularly suitable analytical separation method that can couple very small samples and rapid separations to a wide range of selective and sensitive detection techniques. This paper demonstrates a method for rapid separation and identification of four microcystin variants commonly found in aquatic environments. CE coupled to UV and electrospray ionization time-of-flight mass spectrometry (ESI-TOF) procedures were developed. All four analytes were separated within 6 minutes. The ESI-TOF experiment provides accurate molecular information, which further identifies analytes.

Microbial community composition and bacterioplankton at time series station Helgoland Roads, North Sea

A process of global importance in carbon cycling is the remineralization of algae biomass by heterotrophic bacteria, most notably during massive marine algae blooms. Such blooms can trigger secondary blooms of planktonic bacteria that consist of swift successions of distinct bacterial clades, most prominently members of the Flavobacteriia, Gammaproteobacteria and the alphaproteobacterial Roseobacter clade. This study explores such successions during spring phytoplankton blooms in the southern North Sea (German Bight) for four consecutive years. The surface water samples were taken at Helgoland Island about 40 km offshore in the southeastern North Sea in the German Bight at the station 'Kabeltonne' (54° 11.3' N, 7° 54.0' E) between the main island and the minor island, Düne (German for 'dune') using small research vessels (http://www.awi.de/en/expedition/ships/more-ships.html). Water depths at this site fluctuate from 6 to 10 m over the tidal cycle. Samples were processed as described previously (Teeling et al., 2012; doi:10.7554/eLife.11888.001) in the laboratory of the Biological Station Helgoland within less than two hours after sampling. Assessment of absolute cell numbers and bacterioplankton community composition was carried out as described previously (Thiele et al., 2011; doi:10.1016/B978-0-444-53199-5.00056-7). To obtain total cell numbers, DNA of formaldehyde fixed cells filtered on 0.2 mm pore sized filters was stained with 4',6-diamidino-2-phenylindole (DAPI). Fluorescently labeled cells were subsequently counted on filter sections using an epifluores-cence microscope. Likewise, bacterioplankton community composition was assessed by catalyzedreporter deposition fluorescence in situ hybridization (CARD-FISH) of formaldehyde fixed cells on 0.2 mm pore sized filters.