Seasonal phosphorus and carbon dynamics in a temperate shelf sea (Celtic Sea)

The seasonal cycle of resource availability in shelf seas has a strong selective pressure on phytoplankton diversity and the biogeochemical cycling of key elements, such as carbon (C) and phosphorus (P). Shifts in carbon consumption relative to P availability, via changes in cellular stoichiometry for example, can lead to an apparent ‘excess’ of carbon production. We made measurements of inorganic P (Pi) uptake, in parallel to C-fixation, by plankton communities in the Celtic Sea (NW European Shelf) in spring (April 2015), summer (July 2015) and autumn (November 2014). Short-term (<8 h) Pi-uptake coupled with dissolved organic phosphorus (DOP) release, in parallel to net (24 h) primary production (NPP), were all measured across an irradiance gradient designed to typify vertically and seasonally varying light conditions. Rates of Pi-uptake were highest during spring and lowest in the low light conditions of autumn, although biomass-normalised Pi-uptake was highest in the summer. The release of DOP was highest in November and declined to low levels in July, indicative of efficient utilization and recycling of the low levels of Pi available. Examination of daily turnover times of the different particulate pools, including estimates of phytoplankton and bacterial carbon, indicated a differing seasonal influence of autotrophs and heterotrophs in P-dynamics, with summer conditions associated with a strong bacterial influence and the early spring period with fast growing phytoplankton. These seasonal changes in autotrophic and heterotrophic influence, coupled with changes in resource availability (Pi, light) resulted in seasonal changes in the stoichiometry of NPP to daily Pi-uptake (C:P ratio); from relatively C-rich uptake in November and late April, to P-rich uptake in early April and July. Overall, these results highlight the seasonally varying influence of both autotrophic and heterotrophic components of shelf sea ecosystems on the relative uptake of C and P

Reprint of: High prey-predator size ratios and unselective feeding in copepods: A seasonal comparison of five species with contrasting feeding modes

There has been an upsurge of interest in trait-based approaches to zooplankton, modelling the seasonal changes in the feeding modes of zooplankton in relation to phytoplankton traits such as size or motility. We examined this link at two English Channel plankton monitoring sites south of Plymouth (L4 and E1). At L4 there was a general transition from diatoms in spring to motile microplankton in summer and autumn, but this was not mirrored in the succession of copepod feeding traits; for example the ambushing Oithona similis dominated during the spring diatom bloom. At nearby E1 we measured seasonality of food and grazers, finding strong variation between 2014 and 2015 but overall low mesozooplankton biomass (median 4.5 mg C m−3). We also made a seasonal grazing study of five copepods with contrasting feeding modes (Calanus helgolandicus, Centropages typicus, Acartia clausi, Pseudocalanus elongatus and Oithona similis), counting the larger prey items from the natural seston. All species of copepod fed on all food types and differences between their diets were only subtle; the overriding driver of diet was the composition of the prey field. Even the smaller copepods fed on copepod nauplii at significant rates, supporting previous suggestions of the importance of intra-guild predation. All copepods, including O. similis, were capable of tackling extremely long (>500 µm) diatom chains at clearance rates comparable to those on ciliates. Maximum observed prey:predator length ratios ranged from 0.12 (C. helgolandicus) up to 0.52 (O. similis). Unselective feeding behaviour and the ability to remove highly elongated cells have implications for how copepod feeding is represented in ecological and biogeochemical models

Abundance of a chlorophyll a precursor and the oxidation product hydroxychlorophyll a during seasonal phytoplankton community progression in the Western English Channel

This study presents the first in-situ measurements of the chlorophyll a oxidation product, hydroxychlorophyll a as well as the chlorophyll a precursor, chlorophyll aP276 conducted over an annual cycle. Chlorophyll a oxidation products, such as hydroxychlorophyll a may be associated with the decline of algal populations and can act as an initial step in the degradation of chlorophyll a into products which can be found in the geochemical record, important for studying past climate change events. Here, hydroxychlorophyll a and chlorophyll aP276 were measured at the long-term monitoring station L4, Western Channel Observatory (UK, www.westernchannelobservatory.org) over an annual cycle (2012). Weekly measurements of phytoplankton species composition and abundance enabled detailed analysis of possible sources of hydroxychlorophyll a. Dinoflagellates, 2 diatom species, the prymnesiophyte Phaeocystis spp. and the coccolithophorid Emiliania huxleyi were all associated with hydroxychlorophyll a occurrence. However, during alternate peaks in abundance of the diatoms, no association with hydroxychlorophyll a occurred, indicating that the oxidation of chlorophyll a was dependant not only on species but also on additional factors such as the mode of mortality, growth limiting factor (i.e. nutrient concentration) or phenotypic plasticity. Surface sediment samples contained 10 times more hydroxychlorophyll a (relative to chlorophyll a) than pelagic particulate samples, indicating that more chlorophyll a oxidation occurred during sedimentation or at the sediment-water interface, than in the pelagic environment. In addition, chlorophyll aP276 correlated with chl-a concentration, thus supporting its assignment as a chl-a precursor

Effects of elevated CO2 on phytoplankton community biomass and species composition during a spring Phaeocystis spp. bloom in the western English Channel

A 21-year time series of phytoplankton community structure was analysed in relation to Phaeocystis spp. to elucidate its contribution to the annual carbon budget at station L4 in the western English Channel (WEC). Between 1993–2014 Phaeocystis spp. contributed ∼4.6% of the annual phytoplankton carbon and during the March − May spring bloom, the mean Phaeocystis spp. biomass constituted 17% with a maximal contribution of 47% in 2001. Upper maximal weekly values above the time series mean ranged from 63 to 82% of the total phytoplankton carbon (∼42–137 mg carbon (C) m −3 ) with significant inter-annual variability in Phaeocystis spp. Maximal biomass usually occurred by the end of April, although in some cases as early as mid-April (2007) and as late as late May (2013). The effects of elevated pCO 2 on the Phaeocystis spp. spring bloom were investigated during a fifteen-day semi-continuous microcosm experiment. The phytoplankton community biomass was estimated at ∼160 mg C m −3 and was dominated by nanophytoplankton (40%, excluding Phaeocystis spp.), Phaeocystis spp. (30%) and cryptophytes (12%). The smaller fraction of the community biomass comprised picophytoplankton (9%), coccolithophores (3%), Synechococcus (3%), dinoflagellates (1.5%), ciliates (1%) and diatoms (0.5%). Over the experimental period, total biomass increased significantly by 90% to ∼305 mg C m −3 in the high CO 2 treatment while the ambient pCO 2 control showed no net gains. Phaeocystis spp. exhibited the greatest response to the high CO 2 treatment, increasing by 330%, from ∼50 mg C m −3 to over 200 mg C m −3 and contributing ∼70% of the total biomass. Taken together, the results of our microcosm experiment and analysis of the time series suggest that a future high CO 2 scenario may favour dominance of Phaeocystis spp. during the spring bloom. This has significant implications for the formation of hypoxic zones and the alteration of food web structure including inhibitory feeding effects and lowered fecundity in many copepod species

Learning biophysically-motivated parameters for alpha helix prediction

<p>Abstract</p> <p>Background</p> <p>Our goal is to develop a state-of-the-art protein secondary structure predictor, with an intuitive and biophysically-motivated energy model. We treat structure prediction as an optimization problem, using parameterizable cost functions representing biological "pseudo-energies". Machine learning methods are applied to estimate the values of the parameters to correctly predict known protein structures.</p> <p>Results</p> <p>Focusing on the prediction of alpha helices in proteins, we show that a model with 302 parameters can achieve a Q_{<it>α </it>}value of 77.6% and an SOV_{<it>α </it>}value of 73.4%. Such performance numbers are among the best for techniques that do not rely on external databases (such as multiple sequence alignments). Further, it is easier to extract biological significance from a model with so few parameters.</p> <p>Conclusion</p> <p>The method presented shows promise for the prediction of protein secondary structure. Biophysically-motivated elementary free-energies can be learned using SVM techniques to construct an energy cost function whose predictive performance rivals state-of-the-art. This method is general and can be extended beyond the all-alpha case described here.</p

Causal networks of phytoplankton diversity and biomass are modulated by environmental context

Untangling causal links and feedbacks among biodiversity, ecosystem functioning, and environmental factors is challenging due to their complex and context-dependent interactions (e.g., a nutrient-dependent relationship between diversity and biomass). Consequently, studies that only consider separable, unidirectional effects can produce divergent conclusions and equivocal ecological implications. To address this complexity, we use empirical dynamic modeling to assemble causal networks for 19 natural aquatic ecosystems (N24◦~N58◦) and quantified strengths of feedbacks among phytoplankton diversity, phytoplankton biomass, and environmental factors. Through a cross-system comparison, we identify macroecological patterns; in more diverse, oligotrophic ecosystems, biodiversity effects are more important than environmental effects (nutrients and temperature) as drivers of biomass. Furthermore, feedback strengths vary with productivity. In warm, productive systems, strong nitrate-mediated feedbacks usually prevail, whereas there are strong, phosphate-mediated feedbacks in cold, less productive systems. Our findings, based on recovered feedbacks, highlight the importance of a network view in future ecosystem management

Coupled dynamics of dimethylsulfoniopropionate and dimethylsulfide cycling and the microbial food web in surface waters of the North Atlantic.

Oceanic dimethylsulfide (DMS), the main natural source of sulfur to the global atmosphere, is suggested to play a key role in the interaction between marine biota and climate. Its biochemical precursor is dimethylsulfoniopropionate (DMSP), a globally distributed, intracellular constituent in marine phytoplankton. During a multidisciplinary Lagrangian experiment in the subpolar North Atlantic, we determined the fluxes of DMSP and DMS through phytoplankton, microzooplankton, and bacterioplankton and compared them with concurrent carbon and sulfur fluxes through primary and secondary productions, grazing, and release and use of dissolved organic matter. We found that DMSP and derivatives contributed most (48-100%) of the sulfur fluxes and 5-15% of the carbon fluxes. Our findings highlight DMSP as a prominent player in pelagic biogeochemical pumps, especially as a major carrier in organic sulfur cycling. Also, our results illustrate the key role played by microzooplankton and heterotrophic bacteria (hence the microbial food web) in controlling the amount of phytoplanktonic DMSP that ultimately vents to the atmosphere in the form of DMS