Temporal variability in total, micro- and nano-phytoplankton primary production at a coastal site in the Western English Channel

Primary productivity and subsequent carbon cycling in the coastal zone have a significant impact on the global carbon budget. It is currently unclear how anthropogenic activity could alter these budgets but long term coastal time series of hydrological, biogeochemical and biological measurements represent a key means to better understand past drivers, and hence to predicting future seasonal and inter-annual variability in carbon fixation in coastal ecosystems. An 8-year time series of primary production from 2003 to 2010, estimated using a recently developed absorption-based algorithm, was used to determine the nature and extent of change in primary production at a coastal station (L4) in the Western English Channel (WEC). Analysis of the seasonal and inter-annual variability in production demonstrated that on average, nano- and pico-phytoplankton account for 48% of the total carbon fixation and micro-phytoplankton for 52%. A recent decline in the primary production of nano- and pico-phytoplankton from 2005 to 2010 was observed, corresponding with a decrease in winter nutrient concentrations and a decrease in the biomass of Phaeocystis sp. Micro-phytoplankton primary production (PPM) remained relatively constant over the time series and was enhanced in summer during periods of high precipitation. Increases in sea surface temperature, and decreases in wind speeds and salinity were associated with later spring maxima in PPM. Together these trends indicate that predicted increases in temperature and decrease in wind speeds in future would drive later spring production whilst predicted increases in precipitation would also continue these blooms throughout the summer at this site.

RRS Discovery DY021 Cruise Report, March 2015

The Shelf Sea Biogeochemistry research programme directly relates to the delivery of the NERC Earth system science theme and aims to provide evidence that supports a number of marine policy areas and statutory requirements, such as the Marine Strategy Framework Directive and Marine and Climate Acts. The shelf seas are highly productive compared to the open ocean, a productivity that underpins more than 90 per cent of global fisheries. Their importance to society extends beyond food production to include issues of biodiversity, carbon cycling and storage, waste disposal, nutrient cycling, recreation and renewable energy resources. The shelf seas have been estimated to be the most valuable biome on Earth, but they are under considerable stress, as a result of anthropogenic nutrient loading, overfishing, habitat disturbance, climate change and other impacts. However, even within the relatively well-studied European shelf seas, fundamental biogeochemical processes are poorly understood. For example: the role of shelf seas in carbon storage; in the global cycles of key nutrients (nitrogen, phosphorus, silicon and iron); and in determining primary and secondary production, and thereby underpinning the future delivery of many other ecosystem services. Improved knowledge of such factors is not only required by marine policymakers; it also has the potential to increase the quality and cost-effectiveness of management decisions at the local, national and international levels under conditions of climate change. The Shelf Sea Biogeochemistry research programme will take a holistic approach to the cycling of nutrients and carbon and the controls on primary and secondary production in UK and European shelf seas, to increase understanding of these processes and their role in wider biogeochemical cycles. It will thereby significantly improve predictive marine biogeochemical and ecosystem models over a range of scales. The scope of the programme includes exchanges with the open ocean (transport on and off the shelf to a depth of around 500m), together with cycling, storage and release processes on the shelf slope, and air-sea exchange of greenhouse gases (carbon dioxide and nitrous oxide). The DY021 cruise is the first of the 2015 Benthic SSB cruises to investigate the 4 main ‘representative’ sites in the Celtic Sea that will represent all the various sediment types found in the whole area, these being Mud, San, Sandy-Mud and Muddy-Sand. The cruise will also carry out complimentary sampling at the Pelagic SSB programme main site called CANDYFLOSS in the central Shelf area in order to better link the Benthic and Pelagic programmes.

Mercury presence and speciation in the South Atlantic Ocean along the 40°S transect

Mercury (Hg) natural biogeochemical cycle is complex and a significant portion of biological and chemical transformation occurs in the marine environment. To better understand the presence and abundance of Hg species in the remote ocean regions, waters of South Atlantic Ocean along 40°S parallel were investigated during UK-GEOTRACES cruise GA10. Total mercury (THg), methylated mercury (MeHg), and dissolved gaseous mercury (DGM) concentrations were determined. The concentrations were very low in the range of pg/L (femtomolar). All Hg species had higher concentration in western than in eastern basin. THg did not appear to be a useful geotracer. Elevated methylated Hg species were commonly associated with low-oxygen water masses and occasionally with peaks of chlorophyll a, both involved with carbon (re)cycling. The overall highest MeHg concentrations were observed in themixed layer (500m) and in the vicinity of the Gough Island. Conversely, DGM concentrations showed distinct layering and differed between the water masses in a nutrient-like manner. DGM was lowest at surface, indicating degassing to the atmosphere, and was highest in the Upper Circumpolar Deep Water, where the oxygen concentration was lowest. DGM increased also in Antarctic Bottom Water. At one station, dimethylmercury was determined and showed increase in region with lowest oxygen saturation. Altogether, our data indicate that the South Atlantic Ocean could be a source of Hg to the atmosphere and that its biogeochemical transformations depend primarily upon carbon cycling and are thereby additionally prone to global ocean change.

Patrons saisonniers de transformation du carbone et efficacité métabolique des communautés bactériennes du golfe d’Amundsen, Arctique canadien

Les réchauffements climatiques associés aux activités anthropiques ont soumis les écosystèmes arctiques à des changements rapides qui menacent leur stabilité à court terme. La diminution dramatique de la banquise arctique est une des conséquences les plus concrètes de ce réchauffement. Dans ce contexte, comprendre et prédire comment les systèmes arctiques évolueront est crucial, surtout en considérant comment les flux de carbone (C) de ces écosystèmes - soit des puits nets, soit des sources nettes de CO2 pour l'atmosphère - pourraient avoir des répercussions importantes sur le climat. Le but de cette thèse est de dresser un portrait saisonnier de l’activité bactérienne afin de déterminer l’importance de sa contribution aux flux de carbone en Arctique. Plus spécifiquement, nous caractérisons pour la première fois la respiration et le recours à la photohétérotrophie chez les microorganismes du golfe d’Amundsen. Ces deux composantes du cycle du carbone demeurent peu décrites et souvent omises des modèles actuels, malgré leur rôle déterminant dans les flux de C non seulement de l’Arctique, mais des milieux marins en général. Dans un premier temps, nous caractérisons la respiration des communautés microbiennes (RC) des glaces de mer. La connaissance des taux de respiration est essentielle à l’estimation des flux de C, mais encore limitée pour les milieux polaires. En effet, les études précédentes dans le golfe d’Amundsen n’ont pas mesuré la RC. Par la mesure de la respiration dans les glaces, nos résultats montrent des taux élevés de respiration dans la glace, de 2 à 3 fois supérieurs à la colonne d'eau, et une production bactérienne jusqu’à 25 fois plus importante. Ces résultats démontrent que la respiration microbienne peut consommer une proportion significative de la production primaire (PP) des glaces et pourrait jouer un rôle important dans les flux biogéniques de CO2 entre les glaces de mer et l’atmosphère (Nguyen et Maranger, 2011). Dans un second temps, nous mesurons la respiration des communautés microbiennes pélagiques du golfe d’Amundsen pendant une période de 8 mois consécutif, incluant le couvert de glace hivernal. En mesurant directement la consommation d'O2, nous montrons une RC importante, mesurable tout au long de l’année et dépassant largement les apports en C de la production primaire. Globalement, la forte consommation de C par les communautés microbiennes suggère une forte dépendance sur recyclage interne de la PP locale. Ces observations ont des conséquences importantes sur notre compréhension du potentiel de séquestration de CO2 par les eaux de l’Océan Arctique (Nguyen et al. 2012). Dans un dernier temps, nous déterminons la dynamique saisonnière de présence (ADN) et d’expression (ARN) du gène de la protéorhodopsine (PR), impliqué dans la photohétérotrophie chez les communautés bactérienne. Le gène de la PR, en conjonction avec le chromophore rétinal, permet à certaines bactéries de capturer l’énergie lumineuse à des fins énergétiques ou sensorielles. Cet apport supplémentaire d’énergie pourrait contribuer à la survie et prolifération des communautés qui possèdent la protéorhodopsine. Bien que détectée dans plusieurs océans, notre étude est une des rares à dresser un portrait saisonnier de la distribution et de l’expression du gène en milieu marin. Nous montrons que le gène de la PR est présent toute l’année et distribué dans des communautés diversifiées. Étonnamment, l’expression du gène se poursuit en hiver, en absence de lumière, suggérant soit qu’elle ne dépend pas de la lumière, ou que des sources de photons très localisées justifie l’expression du gène à des fins sensorielles et de détection (Nguyen et al., soumis au journal ISME). Cette thèse contribue à la compréhension du cycle du C en Arctique et innove par la caractérisation de la respiration et de l’efficacité de croissance des communautés microbiennes pélagiques et des glaces de mer. De plus, nous montrons pour la première fois une expression soutenue de la protéorhodopsine en Arctique, qui pourrait moduler la consommation de C par la respiration et justifier son inclusion éventuelle dans les modélisations du cycle du C. Dans le contexte des changements climatiques, il est clair que l'importance de l’activité bactérienne a été sous-estimée et aura un impact important dans le bilan de C de l'Arctique.

Chemical Evaluation of Selected Organics and Trace Metals in the Mangrove Macroflora Of Cochin

Mangroves are considered to play a significant role in global carbon cycling. Themangrove forests would fix CO2 by photosynthesis into mangrove lumber and thus decrease the possibility of a catastrophic series of events - global warming by atmospheric CO2, melting of the polar ice caps, and inundation of the great coastal cities of the world. The leaf litter and roots are the main contributors to mangrove sediments, though algal production and allochthonous detritus can also be trapped (Kristensen et al, 2008) by mangroves due to their high organic matter content and reducing nature are excellent metal retainers. Environmental pollution due to metals is of major concern. This is due to the basic fact that metals are not biodegradable or perishable the way most organic pollutants are. While most organic toxicants can be destroyed by combustion and converted into compounds such as C0, C02, SOX, NOX, metals can't be destroyed. At the most the valance and physical form of metals may change. Concentration of metals present naturally in air, water and soil is very low. Metals released into the environment through anthropogenic activities such as burning of fossils fuels, discharge of industrial effluents, mining, dumping of sewage etc leads to the development of higher than tolerable or toxic levels of metals in the environment leading to metal pollution. Of course, a large number of heavy metals such as Fe, Mn, Cu, Ni, Zn, Co, Cr, Mo, and V are essential to plants and animals and deficiency of these metals may lead to diseases, but at higher levels, it would lead to metal toxicity. Almost all industrial processes and urban activities involve release of at least trace quantities of half a dozen metals in different forms. Heavy metal pollution in the environment can remain dormant for a long time and surface with a vengeance. Once an area gets toxified with metals, it is almost impossible to detoxify it. The symptoms of metal toxicity are often quite similar to the symptoms of other common diseases such as respiratory problems, digestive disorders, skin diseases, hypertension, diabetes, jaundice etc making it all the more difficult to diagnose metal poisoning. For example the Minamata disease caused by mercury pollution in addition to affecting the nervous system can disturb liver function and cause diabetes and hypertension. The damage caused by heavy metals does not end up with the affected person. The harmful effects can be transferred to the person's progenies. Ironically heavy metal pollution is a direct offshoot of our increasing ability to mass produce metals and use them in all spheres of existence. Along with conventional physico- chemical methods, biosystem approachment is also being constantly used for combating metal pollution

Mesozooplankton of the Arabian Sea and the Bay of Bengal with special reference to planktonic ostracods

The Arabian Sea and the Bay of Bengal are both highly dynamic ecosystems, due to the seasonally reversing monsoon winds, but the processes affecting the mesozooplankton community remain poorly understood. These are important basins exhibiting enhanced biological production as a result of upwelling, winter cooling and other episodic events such as eddies and gyres. Zooplankters are primarily the prey for almost all fish larvae. Seasonal changes in the biogeochemical processes can strongly affect zooplankton density and distribution, which in turn, strongly affect the larval growth, and consequently, the pelagic fish recruitment. It is clear that plankton biomass and biogeochemical fluxes are not in steady state. Acoustic data on mesozooplankton abundance suggests that they also exist in the mesopelagic zone. Earlier studies were confined only to the upper 200 m and hence the structure of mesozooplankton community in the deeper layers was not well known. Copepods are the dominant mesoplankton group, and therefore the majority of the studies were focused on them. The planktonic ostracods are the second major crustacean group and at times, their swarms can outnumber all other planktonic groups. The understanding of the community structure of the ostracods is essential to establish their role in the marine food web. Mesozooplankton is responsible for the vertical flux of organic matter produced by phytoplankton and is assumed to be equivalent to new production (Eppley & Peterson, 1979). Since the fate of newly produced organic matter depends upon their consumers, the zooplankton biomass must be estimated in size fractions or taxonomic components to understand the vertical flux of organic carbon. It is thus important to update our knowledge on different groups of zooplankton on the basis of seasonal and temporal distribution. The distribution in space and time is essential for modeling the carbon cycling that structure the marine ecosystems

Earthworms produce granules of intricately zoned calcite

Earthworms of the family Lumbricidae, which includes many common species, produce and secrete up to millimeter-sized calcite granules, and the intricate fine-scale zoning of their constituent crystals is unique for a biomineral. Granule calcite is produced by crystallization of amorphous calcium carbonate (ACC) that initially precipitates within the earthworm calciferous glands, then forms protogranules by accretion on quartz grain cores. Crystallization of ACC is mediated by migrating fluid films and is largely complete within 24 11 of ACC production and before granules leave the earthworm. Variations in the density of defects formed as a byproduct of trace element incorporation during calcite crystall growth have generated zoning that can be resolved by cathodoluminescence imaging at ultraviolet to blue wavelengths and using the novel technique of scanning electron microscope charge contrast imaging. Mapping of calcite crystal orientations by electron backscatter diffraction reveals an approximate radial fabric to the granules that reflects crystal growth from internal nucleation sites toward their margins. The survival within granules of ACC inclusions for months after they enter soils indicates that they crystallize only within the earthworm and in the presence of fluids containing biochemical catalysts. The earthworm probably promotes crystallization of ACC in order to prevent remobilization of the calcium carbonate by dissolution. Calcite granules vividly illustrate the role of transient precursors in biomineralization, but the underlying question of why earth-worms produce granules in volumes sufficient to have a measurable impact on soil carbon cycling remains to be answered.

Fine-root turnover rates of European forests revisited: an analysis of data from sequential coring and ingrowth cores

Background and Aims Forest trees directly contribute to carbon cycling in forest soils through the turnover of their fine roots. In this study we aimed to calculate root turnover rates of common European forest tree species and to compare them with most frequently published values. Methods We compiled available European data and applied various turnover rate calculation methods to the resulting database. We used Decision Matrix and Maximum-Minimum formula as suggested in the literature. Results Mean turnover rates obtained by the combination of sequential coring and Decision Matrix were 0.86 yr−1 for Fagus sylvatica and 0.88 yr−1 for Picea abies when maximum biomass data were used for the calculation, and 1.11 yr−1 for both species when mean biomass data were used. Using mean biomass rather than maximum resulted in about 30 % higher values of root turnover. Using the Decision Matrix to calculate turnover rate doubled the rates when compared to the Maximum-Minimum formula. The Decision Matrix, however, makes use of more input information than the Maximum-Minimum formula. Conclusions We propose that calculations using the Decision Matrix with mean biomass give the most reliable estimates of root turnover rates in European forests and should preferentially be used in models and C reporting.

Interacting controls on innate sources of CO2 efflux from a calcareous arid zone soil under experimental acidification and wetting

More than half of global soil carbon is stored as carbonates, primarily in arid and semi-arid zones. Climate change models predict more frequent and severe rainfall events in some parts of the globe, many of which are dominated by calcareous soils. Such events trigger substantial increases in soil CO2 efflux. We hypothesised that the primary source of CO2 emissions from calcareous, arid zone soil during a single wetting event is abiotic and that soil acidification and wetting have a positive, potentially interacting, effect. We manipulated soil pH, soil moisture, and controlled soil respiration by gamma irradiating half of an 11 day incubation experiment. All manipulated experimental treatments had a rapid and enormous effect on CO2 emission. Respiration contributed ca. 5% of total CO2 efflux; the major source (carbonate buffering) varied depending on the extent of acidification and wetting. Maximum CO2 efflux occurred when pH was lowest and at intermediate matric potential. CO2 efflux was lowest at native pH when soil was air dry. Our data suggest that there may be an underestimate of soil-atmosphere carbon fluxes in arid ecosystems with calcareous soils. There is also a clear potential that these soils may become net carbon sources depending on changes in rainfall patterns, rainfall acidity, and future land management. Our findings have major implications for carbon cycling in arid zone soil and further study of carbon dynamics in these terrestrial systems at a landscape level will be required if we are to improve global climate and carbon cycling models.

Spatial variability models of CO2 emissions from soils colonized by grass (Deschampsia antarctica) and moss (Sanionia uncinata) in Admiralty Bay, King George Island

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

The Microbiome of Brazilian Mangrove Sediments as Revealed by Metagenomics

Here we embark in a deep metagenomic survey that revealed the taxonomic and potential metabolic pathways aspects of mangrove sediment microbiology. The extraction of DNA from sediment samples and the direct application of pyrosequencing resulted in approximately 215 Mb of data from four distinct mangrove areas (BrMgv01 to 04) in Brazil. The taxonomic approaches applied revealed the dominance of Deltaproteobacteria and Gammaproteobacteria in the samples. Paired statistical analysis showed higher proportions of specific taxonomic groups in each dataset. The metabolic reconstruction indicated the possible occurrence of processes modulated by the prevailing conditions found in mangrove sediments. In terms of carbon cycling, the sequences indicated the prevalence of genes involved in the metabolism of methane, formaldehyde, and carbon dioxide. With respect to the nitrogen cycle, evidence for sequences associated with dissimilatory reduction of nitrate, nitrogen immobilization, and denitrification was detected. Sequences related to the production of adenylsulfate, sulfite, and H2S were relevant to the sulphur cycle. These data indicate that the microbial core involved in methane, nitrogen, and sulphur metabolism consists mainly of Burkholderiaceae, Planctomycetaceae, Rhodobacteraceae, and Desulfobacteraceae. Comparison of our data to datasets from soil and sea samples resulted in the allotment of the mangrove sediments between those samples. The results of this study add valuable data about the composition of microbial communities in mangroves and also shed light on possible transformations promoted by microbial organisms in mangrove sediments.

Factors controlling water-column respiration in rivers of the central and southwestern Amazon Basin

We examined the factors controlling the variability in water-column respiration rates in Amazonian rivers. Our objectives were to determine the relationship between respiration rates and the in situ concentrations of the size classes of organic carbon (OC), and the biological source (C-3 and C-4 plants and phytoplankton) of organic matter (OM) supporting respiration. Respiration was measured along with OC size fractions and dissolved oxygen isotopes (delta O-18-O-2) in rivers of the central and southwestern Amazon Basin. Rates ranged from 0.034 mu mol O-2 L-1 h(-1) to 1.78 mu mol O-2 L-1 h(-1), and were four-fold higher in rivers with evidence of photosynthetic production (demonstrated by delta O-18-O-2<24.2 parts per thousand) as compared to rivers lacking such evidence (delta O-18-O-2>24.2 parts per thousand; 1.35 +/- 0.22 vs. 0.30 +/- 0.29 mu mol L-1 h(-1)). Rates were likely elevated in the former rivers, which were all sampled during low water, due to the stimulation of heterotrophic respiration via the supply of a labile, algal-derived substrate and/or the occurrence of autotrophic respiration. The organic composition of fine particulate OM (FPOM) of these rivers is consistent with a phytoplankton origin. Multiple linear regression analysis indicates that [FPOC], C:N-FPOC ratios, and [O-2] account for a high amount of the variability in respiration rates (r(2) = 0.80). Accordingly, FPOC derived from algal sources is associated with elevated respiration rates. The delta C-13 of respiration-derived CO2 indicates that the role of phytoplankton, C-3 plants, and C-4 grasses in supporting respiration is temporally and spatially variable. Future scaling work is needed to evaluate the significance of phytoplankton production to basin-wide carbon cycling.

Warming alters photosynthetic rates of sub-boreal peatland vegetation

Boreal peatlands are important in the global carbon cycle. Despite covering only 3% of the global land area, peatlands store approximately one third of all soil carbon. Temperature is one of the major drivers in peatland carbon cycling as it affects both plant production and CO2 fluxes from soils. However, it is relatively unknown how boreal peatland plant photosynthesis is affected by higher temperatures. Therefore, we measured plant photosynthetic rates under two different warming treatments in a poor fen in Northern Michigan. Eighteen plots were established that were divided into three treatments: control, open-top chamber (OTC) warming and infrared (IR) lamp warming. Previous work at this site has shown that there was a significant increase in canopy and peat temperature with IR warming (5°C and 1.4°C respectively), while the OTC’s had mixed overall warming. Plots were divided equally into lawns and hummocks. We measured mid-day carbon dioxide (CO2) uptake on sedges (Carex utriculata), shrubs (Chamaedaphne calyculata) and Sphagnum mosses. Sphagnum moss net primary production (NPP) was also measured with cranked wires and compared with CO2 uptake. Our results indicate that there was no significant difference in sedge CO2 uptake, while shrub CO2 uptake significantly decreased with warming. A significant increase occurred in Sphagnum moss gross ecosystem production (GEP), ecosystem respiration (ER) and net ecosystem exchange (NEE). Contrary to the positive CO2 exchange of Sphagnum, overall NPP decreased significantly in hummocks with both warming treatments. The results of the study indicate that temperature partly limits the photosynthetic capacity of plants in sub-boreal peatlands, but not all species respond similarly to higher temperatures.

BEYOND ROOTS ALONE: NOVEL METHODOLOGIES FOR ANALYZING COMPLEX SOIL AND MINIRHIZOTRON IMAGERY USING IMAGE PROCESSING AND GIS TOOLS

Quantifying belowground dynamics is critical to our understanding of plant and ecosystem function and belowground carbon cycling, yet currently available tools for complex belowground image analyses are insufficient. We introduce novel techniques combining digital image processing tools and geographic information systems (GIS) analysis to permit semi-automated analysis of complex root and soil dynamics. We illustrate methodologies with imagery from microcosms, minirhizotrons, and a rhizotron, in upland and peatland soils. We provide guidelines for correct image capture, a method that automatically stitches together numerous minirhizotron images into one seamless image, and image analysis using image segmentation and classification in SPRING or change analysis in ArcMap. These methods facilitate spatial and temporal root and soil interaction studies, providing a framework to expand a more comprehensive understanding of belowground dynamics.

Unraveling environmental drivers of a recent increase in Swiss fungi fruiting

Disentangling biotic and abiotic drivers of wild mushroom fruiting is fraught with difficulties because mycelial growth is hidden belowground, symbiotic and saprotrophic supply strategies may interact, and myco-ecological observations are often either discontinuous or too short. Here, we compiled and analyzed 115 417 weekly fungal fruit body counts from permanent Swiss inventories between 1975 and 2006. Mushroom fruiting exhibited an average autumnal delay of 12 days after 1991 compared with before, the annual number of fruit bodies increased from 1801 to 5414 and the mean species richness doubled from 10 to 20. Intra- and interannual coherency of symbiotic and saprotrophic mushroom fruiting, together with little agreement between mycorrhizal yield and tree growth suggests direct climate controls on fruit body formation of both nutritional modes. Our results contradict a previously reported declining of mushroom harvests and propose rethinking the conceptual role of symbiotic pathways in fungi-host interaction. Moreover, this conceptual advancement may foster new cross-disciplinary research avenues, and stimulate questions about possible amplifications of the global carbon cycle, as enhanced fungal production in moist mid-latitude forests rises carbon cycling and thus increases greenhouse gas exchanges between terrestrial ecosystems and the atmosphere.