Mediterranean Center for Marine and Environmental Research

Barcelona, Spain

Mediterranean Center for Marine and Environmental Research

Barcelona, Spain
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Aguileta G.,Center for Genomic Regulation | Aguileta G.,University Pompeu Fabra | Aguileta G.,French National Institute for Agricultural Research | De Vienne D.M.,Center for Genomic Regulation | And 11 more authors.
Genome Biology and Evolution | Year: 2014

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.


Ross O.N.,Mediterranean Center for Marine and Environmental Research | Geider R.J.,University of Essex | Berdalet E.,CSIC - Institute of Marine Sciences | Artigas M.L.,CSIC - Institute of Marine Sciences | Piera J.,Mediterranean Center for Marine and Environmental Research
Marine Ecology Progress Series | Year: 2011

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 photo - inhibition, 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. (2011; Mar Ecol Prog Ser 435:33-45). © Inter-Research 2011.


Ross O.N.,Mediterranean Center for Marine and Environmental Research | Geider R.J.,University of Essex | Piera J.,Mediterranean Center for Marine and Environmental Research
Marine Ecology Progress Series | Year: 2011

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). © Inter-Research 2011.


Scott B.E.,University of Aberdeen | Sharples J.,University of Liverpool | Ross O.N.,Mediterranean Center for Marine and Environmental Research | Wang J.,University of Aberdeen | And 3 more authors.
Marine Ecology Progress Series | Year: 2010

The foraging habitats of 7 species of marine apex predators were observed simultaneously in a shallow sea, with continuous measurements taken of the detailed bio-physical water column characteristics to determine habitat preferences. We found the occurrence of small-scale 'hotspots', where 50% of all animals were actively foraging in less than 5% of the 1000 km of transects surveyed. By investigating a contrasting range of foraging strategies across a variety of fisheating seabirds and marine mammals, we determined which habitat characteristics were consistently important across species. A static habitat variable, tidal stratification, log10(h/U3) (h = water depth, U = tidal current amplitude), was found to be the best indicator of the probability of presence and abundance of individual species. All 7 mobile top-predators preferentially foraged within habitats with small-scale (2 to 10 km) patches having (1) high concentrations of chlorophyll in the sub-surface chlorophyll maximum (CHLmax) and (2) high variance in bottom topography, with different species preferring to forage in different locations within these habitats. Patchiness of CHLmax was not associated with the locations of strong horizontal temperature gradients (fronts) or high surface chlorophyll values, but instead may be related to areas of high sub-surface primary production due to locally increased vertical mixing. These small-scale areas represent a newly identified class of spatially important location that may play a critical role within the trophic coupling of shallow seas. Such subsurface hotspots may represent the limited locations where the majority of predator-prey interactions occur, despite making up only a small percentage of the marine environment. © Inter-Research 2010 · www.int-res.com.

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