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13 pages, 7 figures, 3 tables ; The estimation of in situ phytoplankton primary production is pivotal to many questions in biological oceanography and marine ecology both in a local and global context. Applications range from earth system modelling, the characterisation of aquatic ecosystem dynamics, or the local management of water quality. A common approach for estimating in situ primary production is to incubate natural phytoplankton assemblages in clear bottles at a range of fixed depths and to measure the uptake of carbon (14C) during the incubation period (typically 24 h). One of the main concerns with using fixed-depth bottle incubations is whether stranding samples at fixed depths biases the measured CO2 fixation relative to the 'true' in situ mixed conditions. Here we employ an individual based turbulence and photosynthesis model, which also accounts for photoacclimation and -inhibition, to examine whether the in vitro productivity estimates obtained from fixed-depth incubations are representative of the in situ productivity in a freely mixing water column. While previous work suggested that in vitro estimates could either over- or underestimate the in situ productivity, we show that the errors due to arresting the incubation bottles at fixed depths are indeed minimal. We present possible explanations for how previous authors could have arrived at contradictory results and discuss whether they might be artefacts related to the particular sampling protocol used. We discuss the errors associated with chlorophyll-based incubation methods for determining in situ phytoplankton growth rates in Ross et al. (2011; Mar Ecol Prog Ser 435:13-31) ; The research leading to these results received funding from the European Union Seventh Framework Programme (FP7/2007-2013) Marie Curie Intra-European Fellowship for Career Development under grant agreement no. 255396 for project AQUALIGHT (www.aqualight. info). R.J.G.'s research on photoacclimation is supported by the UK Natural Environment Research Council (NE/ G003688/ 1). The authors also acknowledge the Spanish funded SUMMER (CTM200803309/MAR) and ANERIS (PIF08-015) projects ; Peer Reviewed

19 pages, 9 figures, 2 tables ; Reliable estimates of in situ phytoplankton growth rates are central to understanding the dynamics of aquatic ecosystems. A common approach for estimating in situ growth rates is to incubate natural phytoplankton assemblages in clear bottles at fixed depths or irradiance levels and measure the change in chlorophyll a (Chl) over the incubation period (typically 24 h). Using a modelling approach, we investigate the accuracy of these Chl-based methods focussing on 2 aspects: (1) in a freely mixing surface layer, the cells are typically not in balanced growth, and with photoacclimation, changes in Chl may yield different growth rates than changes in carbon; and (2) the in vitro methods neglect any vertical movement due to turbulence and its effect on the cells' light history. The growth rates thus strongly depend on the incubation depth and are not necessarily representative of the depth-integrated in situ growth rate in the freely mixing surface layer. We employ an individual based turbulence and photosynthesis model, which also accounts for photoacclimation and photoinhibition, to show that the in vitro Chl-based growth rate can differ both from its carbon-based in vitro equivalent and from the in situ value by up to 100%, depending on turbulence intensity, optical depth of the mixing layer, and incubation depth within the layer. We make recommendations for choosing the best depth for single-depth incubations. Furthermore we demonstrate that, if incubation bottles are being oscillated up and down through the water column, these systematic errors can be significantly reduced. In the present study, we focus on Chl-based methods only, while productivity measurements using carbon-based techniques (e.g. 14C) are discussed in Ross et al. ; This study received funding from the European Union Seventh Framework Programme(FP7/2007–2013) Marie Curie Intra-European Fellowship for Career Development under grant agreement no. 255396 for project AQUALIGHT (www. aqualight. info). R.J.G.'s research on photoacclimation is supported by the UK Natural Environment Research Council (NE/ G003688/ 1). M.L.A. benefited from a FPU doctoral scholarship from the Spanish Ministry of Science and Innovation (MICINN). the authors also acknowledge financial support from the Spanish funded projects SUMMER (CTM2008-03309/MAR), ANERIS (PIF08-015), and ECOALFACS (CTM2009-09581; a project endorsed by the 'Harmful Algal Blooms in Stratified Systems' CRP of the GEOHAB programme). ; Peer reviewed

13 pages, 7 figures, tables, supporting information https://dx.doi.org/10.1038/srep32325 ; Emission of the trace gas dimethylsulphide (DMS) from the ocean influences the chemical and optical properties of the atmosphere, and the olfactory landscape for foraging marine birds, turtles and mammals. DMS concentration has been seen to vary across seasons and latitudes with plankton taxonomy and activity, and following the seascape of ocean's physics. However, whether and how does it vary at the time scales of meteorology and day-night cycles is largely unknown. Here we used high-resolution measurements over time and depth within coherent water patches in the open sea to show that DMS concentration responded rapidly but resiliently to mesoscale meteorological perturbation. Further, it varied over diel cycles in conjunction with rhythmic photobiological indicators in phytoplankton. Combining data and modelling, we show that sunlight switches and tunes the balance between net biological production and abiotic losses. This is an outstanding example of how biological diel rhythms affect biogeochemical processes ; This research has been funded by the successive Spanish Ministries of Science through projects SUMMER (CTM2008-03309/MAR) and PEGASO (CTM2012-37615), and through a PhD scholarship to S.-J.R. M.G. acknowledges the receipt of a Beatriu de Pinós post-doctoral fellowship funded by the Generalitat de Catalunya. Support was also provided to E.S.S. by the U.S. National Science Foundation (grants 0851472 and 1143709). O.N.R. acknowledges financial support from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme FP7/2007–2013/ under REA grant agreement n° 624170 as well as the AMICO-BIO project (12-MCGOT-GMES-1-CVS-047/MEDDE/CNRS-INSU). G.L.P. acknowledges an international mobility scholarship from CONICET (Argentina). A.S.M. acknowledges support from the Ministry of Earth Sciences, Government of India ; Peer Reviewed

15 pages, 4 figures, 3 tables, supplementary material figures S1–S3 and tables S1–S5 http://gbe.oxfordjournals.org/content/6/2/451/suppl/DC1 ; From their origin as an early alpha proteobacterial endosymbiont to their current state as cellular organelles, large-scale genomic reorganization has taken place in the mitochondria of all main eukaryotic lineages. So far, most studies have focused on plant and animal mitochondrial (mt) genomes (mtDNA), but fungi provide new opportunities to study highly differentiated mtDNAs. Here, we analyzed 38 complete fungal mt genomesto investigate the evolution of mtDNA geneorder among fungi. Inparticular, we looked for evidence of nonhomologous intrachromosomal recombination and investigated the dynamics of gene rearrangements. We investigated the effect that introns, intronic open reading frames (ORFs), and repeats may have on gene order. Additionally, we asked whether the distribution of transfer RNAs (tRNAs) evolves independently to that of mt protein-codinggenes. We foundthat fungal mt genomes display remarkable variation between and within the major fungal phyla in terms of gene order, genome size, composition of intergenic regions, and presence of repeats, introns, and associated ORFs. Our results support previous evidence for the presence of mt recombination in all fungal phyla, a process conspicuously lacking in most Metazoa. Overall, the patterns of rearrangements may be explained by the combined influences of recombination (i.e., most likely nonhomologous and intrachromosomal), accumulated repeats, especially at intergenic regions, and to a lesser extent, mobile element dynamics. © The Author(s) 2014 ; This work was supported by a Marie Curie Fellowship from the European Union Seventh Framework Programme (FP7- PEOPLE-2010-IEF-No.274223) to G.A., the European Union Seventh Framework Programme (FP7/2007–2013) Marie Curie Intra-European Fellowship for Career Development under grant agreement no. 255396 to O.N.R., the Agence National de la Recherche (ANR 09-BLAN-Fungi-Sex) and the ERC starting (GenomeFun 309403) to T.Gi., the grants (BIO2012-37161 and BFU2009-09168) from the Spanish Ministry of Economy and Competitiveness to T.Ga., and the National Science Foundation grant (NSF DEB 0747222) to M.E.H. ; Peer Reviewed