The phantom midge menace: Migratory Chaoborus larvae maintain poor ecosystem state in eutrophic inland waters

Chaoborus spp. (phantom midge) are prevalent in eutrophic lakes with methane-rich, oxygen depleted hypolimnion and sediments, and the methane-poor, oxygen-rich epilimnion. Using a combination of experiments and system modelling, we demonstrated that the larvae’s burrowing activities in and out of the sediment perturbed the sediment and reintroduced sequestered phosphorus into the overlying water, thereby exacerbating internal nutrient loading in the water column. Fluxes of sediment methane and other reduced solutes enhanced by the larval bioturbation sustain the hypoxic/anoxic condition below the thermocline. Migrating larvae also directly transported methane in their gas vesicles from the deep water and release it in the surface water, potentially contributing to methane emission to air. As nutrient pollution and climate warming persist or worsen in the coming decades, proliferation of Chaoborus could intensify this positive feedback loop and delay lake recovery

Oxygen fluxes beneath Arctic land-fast ice and pack ice: towards estimates of ice productivity

Sea-ice ecosystems are among the most extensive of Earth's habitats; yet its autotrophic and heterotrophic activities remain poorly constrained. We employed the in situ aquatic eddy-covariance (AEC) O-2 flux method and laboratory incubation techniques ((HCO3-)-C-14, [H-3] thymidine and [H-3] leucine) to assess productivity in Arctic sea-ice using different methods, in conditions ranging from land-fast ice during winter, to pack ice within the central Arctic Ocean during summer. Laboratory tracer measurements resolved rates of bacterial C demand of 0.003-0.166mmolCm(-2)day(-1) and primary productivity rates of 0.008-0.125mmolCm(-2)day(-1) for the different ice floes. Pack ice in the central Arctic Ocean was overall net autotrophic (0.002-0.063mmolCm(-2)day(-1)), whereas winter land-fast ice was net heterotrophic (-0.155mmol C m(-2) day(-1)). AEC measurements resolved an uptake of O-2 by the bottom-ice environment, from similar to-2mmolO(2)m(-2) day(-1) under winter land-fast ice to similar to-6mmolO(2)m(-2)day(-1) under summer pack ice. Flux of O-2-deplete meltwater and changes in water flow velocity masked potential biological-mediated activity. AEC estimates of primary productivity were only possible at one study location. Here, productivity rates of 1.3 +/- 0.9mmolO(2)m(-2)day(-1), much larger than concurrent laboratory tracer estimates (0.03mmolCm(-2)day(-1)), indicate that ice algal production and its importance within the marine Arctic could be underestimated using traditional approaches. Given careful flux interpretation and with further development, the AEC technique represents a promising new tool for assessing oxygen dynamics and sea-ice productivity in ice-covered regions.Peer reviewe

Atmospheric methane flux from bubbling seeps: Spatially extrapolated quantification from a Black Sea shelf area

Bubble transport of methane from shallow seep sites in the Black Sea west of the Crimea Peninsula between 70 and 112 m water depth has been studied by extrapolation of results gained through different hydroacoustic methods and direct sampling. Ship-based hydroacoustic echo sounders can locate bubble releasing seep sites very precisely and facilitate their correlation with geological or other features at the seafloor. Here, the backscatter strength of a multibeam system was integrated with single-beam data to estimate the amount of seeps/m2 for different backscatter intensities, resulting in 2709 vents in total. Direct flux measurements by submersible revealed methane fluxes from individual vents of 0.32–0.85 l/min or 14.5–37.8 mmol/min at ambient pressure and temperature conditions. A conservative estimate of 30 mmol/min per site was used to estimate the flux into the water to be 1219–1355 mmol/s. The flux to the atmosphere was calculated by applying a bubble dissolution model taking release depth, temperature, gas composition, and bubble size spectra into account. The flux into the atmosphere (3930–4533 mol/d) or into the mixed layer (6186–6899 mol/d) from the 21.8 km2 large study area is three times higher than independently measured fluxes of dissolved methane for the same area using geochemical methods (1030–2495 mol/d). The amount of methane dissolving in the mixed layer is 2256–2366 mol/d. This close match shows that the hydroacoustic approach for extrapolating the number of seeps/m2 and the applied bubble dissolution model are suitable to extrapolate methane fluxes over larger areas

Application of Oxygen Eddy Correlation in Aquatic Systems

The eddy correlation technique is rapidly becoming an established method for resolving dissolved oxygen fluxes in natural aquatic systems. This direct and noninvasive determination of oxygen fluxes close to the sediment by simultaneously measuring the velocity and the dissolved oxygen fluctuations has considerable advantages compared to traditional methods. This paper describes the measurement principle and analyzes the spatial and temporal scales of those fluctuations as a function of turbulence levels. The magnitudes and spectral structure of the expected fluctuations provide the required sensor specifications and define practical boundary conditions for the eddy correlation instrumentation and its deployment. In addition, data analysis and spectral corrections are proposed for the usual nonideal conditions, such as the time shift between the sensor pair and the limited frequency response of the oxygen sensor. The consistency of the eddy correlation measurements in a riverine reservoir has been confirmed—observing a night–day transition from oxygen respiration to net oxygen production, ranging from −20 to +5 mmol m−2 day−1—by comparing two physically independent, eddy correlation instruments deployed side by side. The natural variability of the fluctuations calls for at least ∼1 h of flux data record to achieve a relative accuracy of better than ∼20%. Although various aspects still need improvement, eddy correlation is seen as a promising and soon-to-be widely applied method in natural waters

Methanotropic microbial communities associated with bubble plumes above gas seeps in the Black Sea

Bubbles evolving from active gas seeps can be traced by hydroacoustic imaging up to 1000 m high in the Black Sea water column. Although methane concentrations are not distinguishable between the water column above the deep seep and reference sites, atmospheric noble gas measurements clearly show the constant input of gases (mainly methane) via seepage into the Black Sea. Archaea (ANME-1, ANME-2) and methanotrophic bacteria detected with specific 16S rRNA-targeted oligonucleotide probes are related to active gas seeps in the oxic and anoxic water column. It is suggested that methane seeps have a much greater influence on the Black Sea methane budget than previously acknowledged and that ANME-1 and ANME-2 are injected via gas bubbles from the sediment into the anoxic water column mediating methane oxidation. Our results show further that only minor amounts of methane evolving from Black Sea gas seeps reach the atmosphere due to the very effective microbial barrier. Hence only major thermodynamically and/or tectonically triggered gas hydrate dissociation has the potential to induce rapid climate changes as suggested by the “clathrate gun hypothesis.

Stratification strength and light climate explain variation in chlorophyll a at the continental scale in a European multilake survey in a heatwave summer

To determine the drivers of phytoplankton biomass, we collected standardized morphometric, physical, and biological data in 230 lakes across the Mediterranean, Continental, and Boreal climatic zones of the European continent. Multilinear regression models tested on this snapshot of mostly eutrophic lakes (median total phosphorus [TP] = 0.06 and total nitrogen [TN] = 0.7 mg L−1), and its subsets (2 depth types and 3 climatic zones), show that light climate and stratification strength were the most significant explanatory variables for chlorophyll a (Chl a) variance. TN was a significant predictor for phytoplankton biomass for shallow and continental lakes, while TP never appeared as an explanatory variable, suggesting that under high TP, light, which partially controls stratification strength, becomes limiting for phytoplankton development. Mediterranean lakes were the warmest yet most weakly stratified and had significantly less Chl a than Boreal lakes, where the temperature anomaly from the long-term average, during a summer heatwave was the highest (+4°C) and showed a significant, exponential relationship with stratification strength. This European survey represents a summer snapshot of phytoplankton biomass and its drivers, and lends support that light and stratification metrics, which are both affected by climate change, are better predictors for phytoplankton biomass in nutrient-rich lakes than nutrient concentrations and surface temperature.Additional co-authors: Jolanda Verspagen, Maria van Herk, Maria G. Antoniou, Nikoletta Tsiarta, Valerie McCarthy, Victor C. Perello, Danielle Machado-Vieira, Alinne Gurjao de Oliveira, Dubravka Špoljaric Maronic, Filip Stevic, Tanja Žuna Pfeiffer, Itana Bokan Vucelic, Petar Žutinic, Marija Gligora Udovic, Anđelka Plenkovic-Moraj, Ludek Blaha, Rodan Geriš, Markéta Frankova, Kirsten Seestern Christoffersen, Trine Perlt Warming, Tõnu Feldmann, Alo Laas, Kristel Panksep, Lea Tuvikene, Kersti Kangro, Judita Koreiviene, Jurate Karosiene, Jurate Kasperoviciene, Ksenija Savadova-Ratkus, Irma Vitonyte, Kerstin Häggqvist, Pauliina Salmi, Lauri Arvola, Karl Rothhaupt, Christos Avagianos, Triantafyllos Kaloudis, Spyros Gkelis, Manthos Panou, Theodoros Triantis, Sevasti-Kiriaki Zervou, Anastasia Hiskia, Ulrike Obertegger, Adriano Boscaini, Giovanna Flaim, Nico Salmaso, Leonardo Cerasino, Sigrid Haande, Birger Skjelbred, Magdalena Grabowska, Maciej Karpowicz, Damian Chmura, Lidia Nawrocka, Justyna Kobos, Hanna Mazur-Marzec, Pablo Alcaraz-Parraga, Elżbieta Wilk-Wozniak, Wojciech Krzton, Edward Walusiak, Ilona Gagala-Borowska, Joana Mankiewicz-Boczek, Magdalena Toporowska, Barbara Pawlik-Skowronska, Michał Niedzwiecki, Wojciech Pęczuła, Agnieszka Napiorkowska-Krzebietke, Julita Dunalska, Justyna Sienska, Daniel Szymanski, Marek Kruk, Agnieszka Budzynska, Ryszard Goldyn, Anna Kozak, Joanna Rosinska, Elżbieta Szeląg-Wasielewska, Piotr Domek, Natalia Jakubowska-Krepska, Kinga Kwasizur, Beata Messyasz, Aleksandra Pełechata, Mariusz Pełechaty, Mikolaj Kokocinski, Beata Madrecka-Witkowska, Iwona Kostrzewska-Szlakowska, Magdalena Frąk, Agnieszka Bankowska-Sobczak, Michał Wasilewicz, Agnieszka Ochocka, Agnieszka Pasztaleniec, Iwona Jasser, Ana M. Antao-Geraldes, Manel Leira, Vitor Vasconcelos, Joao Morais, Micaela Vale, Pedro M. Raposeiro, Vítor Gonçalves, Boris Aleksovski, Svetislav Krstic, Hana Nemova, Iveta Drastichova, Lucia Chomova, Spela Remec-Rekar, Tina Elersek, Lars-Anders Hansson, Pablo Urrutia-Cordero, Andrea G. Bravo, Moritz Buck, William Colom-Montero, Kristiina Mustonen, Don Pierson, Yang Yang, Christine Edwards, Hannah Cromie, Jordi Delgado-Martín, David García, Jose Luís Cereijo, Joan Gomà, Mari Carmen Trapote, Teresa Vegas-Vilarrúbia, Biel Obrador, Ana García-Murcia, Monserrat Real, Elvira Romans, Jordi Noguero-Ribes, David Parreño Duque, Elísabeth Fernandez-Moran, Barbara Úbeda, José Angel Galvez, Núria Catalan, Carmen Pérez-Martínez, Eloísa Ramos-Rodríguez, Carmen Cillero-Castro, Enrique Moreno-Ostos, José María Blanco, Valeriano Rodríguez, Jorge Juan Montes-Pérez, Roberto L. Palomino, Estela Rodríguez-Pérez, Armand Hernandez, Rafael Carballeira, Antonio Camacho, Antonio Picazo, Carlos Rochera, Anna C. Santamans, Carmen Ferriol, Susana Romo, Juan Miguel Soria, Arda Özen, Tünay Karan, Nilsun Demir, Meryem Beklioglu, Nur Filiz, Eti Levi, Ugur Iskin, Gizem Bezirci, Ülkü Nihan Tavsanoglu, Kemal Çelik, Koray Ozhan, Nusret Karakaya, Mehmet Ali Turan Koçer, Mete Yilmaz, Faruk Maras¸lıoglu, Özden Fakioglu, Elif Neyran Soylu, Meral Apaydın Yagcı, Sakir Çınar, Kadir Çapkın, Abdulkadir Yagcı, Mehmet Cesur, Fuat Bilgin, Cafer Bulut, Rahmi Uysal, Köker Latife, Reyhan Akçaalan, Meriç Albay, Mehmet Tahir Alp, Korhan Özkan, Tugba Ongun Sevindik, Hatice Tunca, Burçin Önem, Hans Paerl, Cayelan C. Carey, Bastiaan W. Ibeling

iTools: A Framework for Classification, Categorization and Integration of Computational Biology Resources

The advancement of the computational biology field hinges on progress in three fundamental directions – the development of new computational algorithms, the availability of informatics resource management infrastructures and the capability of tools to interoperate and synergize. There is an explosion in algorithms and tools for computational biology, which makes it difficult for biologists to find, compare and integrate such resources. We describe a new infrastructure, iTools, for managing the query, traversal and comparison of diverse computational biology resources. Specifically, iTools stores information about three types of resources–data, software tools and web-services. The iTools design, implementation and resource meta - data content reflect the broad research, computational, applied and scientific expertise available at the seven National Centers for Biomedical Computing. iTools provides a system for classification, categorization and integration of different computational biology resources across space-and-time scales, biomedical problems, computational infrastructures and mathematical foundations. A large number of resources are already iTools-accessible to the community and this infrastructure is rapidly growing. iTools includes human and machine interfaces to its resource meta-data repository. Investigators or computer programs may utilize these interfaces to search, compare, expand, revise and mine meta-data descriptions of existent computational biology resources. We propose two ways to browse and display the iTools dynamic collection of resources. The first one is based on an ontology of computational biology resources, and the second one is derived from hyperbolic projections of manifolds or complex structures onto planar discs. iTools is an open source project both in terms of the source code development as well as its meta-data content. iTools employs a decentralized, portable, scalable and lightweight framework for long-term resource management. We demonstrate several applications of iTools as a framework for integrated bioinformatics. iTools and the complete details about its specifications, usage and interfaces are available at the iTools web page http://iTools.ccb.ucla.edu