Mitochondrial physiology

As the knowledge base and importance of mitochondrial physiology to evolution, health and disease expands, the necessity for harmonizing the terminology concerning mitochondrial respiratory states and rates has become increasingly apparent. The chemiosmotic theory establishes the mechanism of energy transformation and coupling in oxidative phosphorylation. The unifying concept of the protonmotive force provides the framework for developing a consistent theoretical foundation of mitochondrial physiology and bioenergetics. We follow the latest SI guidelines and those of the International Union of Pure and Applied Chemistry (IUPAC) on terminology in physical chemistry, extended by considerations of open systems and thermodynamics of irreversible processes. The concept-driven constructive terminology incorporates the meaning of each quantity and aligns concepts and symbols with the nomenclature of classical bioenergetics. We endeavour to provide a balanced view of mitochondrial respiratory control and a critical discussion on reporting data of mitochondrial respiration in terms of metabolic flows and fluxes. Uniform standards for evaluation of respiratory states and rates will ultimately contribute to reproducibility between laboratories and thus support the development of data repositories of mitochondrial respiratory function in species, tissues, and cells. Clarity of concept and consistency of nomenclature facilitate effective transdisciplinary communication, education, and ultimately further discovery

Mitochondrial physiology

As the knowledge base and importance of mitochondrial physiology to evolution, health and disease expands, the necessity for harmonizing the terminology concerning mitochondrial respiratory states and rates has become increasingly apparent. The chemiosmotic theory establishes the mechanism of energy transformation and coupling in oxidative phosphorylation. The unifying concept of the protonmotive force provides the framework for developing a consistent theoretical foundation of mitochondrial physiology and bioenergetics. We follow the latest SI guidelines and those of the International Union of Pure and Applied Chemistry (IUPAC) on terminology in physical chemistry, extended by considerations of open systems and thermodynamics of irreversible processes. The concept-driven constructive terminology incorporates the meaning of each quantity and aligns concepts and symbols with the nomenclature of classical bioenergetics. We endeavour to provide a balanced view of mitochondrial respiratory control and a critical discussion on reporting data of mitochondrial respiration in terms of metabolic flows and fluxes. Uniform standards for evaluation of respiratory states and rates will ultimately contribute to reproducibility between laboratories and thus support the development of data repositories of mitochondrial respiratory function in species, tissues, and cells. Clarity of concept and consistency of nomenclature facilitate effective transdisciplinary communication, education, and ultimately further discovery

Microbial Communities in Sunken Wood Are Structured by Wood-Boring Bivalves and Location in a Submarine Canyon

9 páginas, 3 figuras, 2 tablas.The cornerstones of sunken wood ecosystems are microorganisms involved in cellulose degradation. These can either be free-living microorganisms in the wood matrix or symbiotic bacteria associated with wood-boring bivalves such as emblematic species of Xylophaga, the most common deep-sea woodborer. Here we use experimentally submerged pine wood, placed in and outside the Mediterranean submarine Blanes Canyon, to compare the microbial communities on the wood, in fecal pellets of Xylophaga spp. and associated with the gills of these animals. Analyses based on tag pyrosequencing of the 16S rRNA bacterial gene showed that sunken wood contained three distinct microbial communities. Wood and pellet communities were different from each other suggesting that Xylophaga spp. create new microbial niches by excreting fecal pellets into their burrows. In turn, gills of Xylophaga spp. contain potential bacterial symbionts, as illustrated by the presence of sequences closely related to symbiotic bacteria found in other wood eating marine invertebrates. Finally, we found that sunken wood communities inside the canyon were different and more diverse than the ones outside the canyon. This finding extends to the microbial world the view that submarine canyons are sites of diverse marine life.The work of PE Galand and SK Fagervold was supported by the Agence Nationale de la Recherche (ANR) project MICADO (ANR-11JSV7-003-01). The present work was developed within the framework of the projects PROMETEO (CTM2007-66316-C02-01/MAR) and DOSMARES (CTM2010-21810-C03-03). This paper is also a contribution of D Martin and C Romano to the CRG 2009SRG665 funded by the Generalitat de Catalunya. ANJ was funded within the DIWOOD research project by the Max Planck Gesellschaft; CB was funded within the Cluster of Excellence 0The Ocean in the Earth System0 at Marum, Bremen, by the German Research Foundation (DFG).Peer reviewe

Wooden Stepping Stones: Diversity and Biogeography of Deep-Sea Wood Boring Xylophagaidae (Mollusca: Bivalvia) in the North-East Atlantic Ocean, With the Description of a New Genus

Este artículo contiene 21 páginas, 4 tablas, 6 figuras.Wood boring bivalves of the family Xylophagaidae inhabit sunken wood on the deepsea floor where they play a key role in the degradation of this organic matter in the ocean. The patchiness of wood-fall habitats is impeding targeted sampling and little is therefore known on xylophagaid biology. We investigated for the first time the diversity and biogeography of Xylophagaidae in the NE-Atlantic and the Mediterranean over a broad geographic range and in various water depths using experimental wood deployments. We combined morphological and molecular analyses for species discrimination. A phylogenetic reconstruction based on 18S and 28S rRNA and COI genes revealed non-monophyly of the type genus, Xylophaga Turton (1822), and led us to revise the taxonomy and erect the genus Xylonora gen. nov. COI haplotypes of the most abundant species revealed broad Atlanto-Mediterranean genetic connectivity for Xylophaga dorsalis and Xylonora atlantica new comb., while genetic connectivity appears limited for Abditoconus brava across the entrance of the Mediterranean. We provide the first COI barcode data for Xylophagaidae as a solid base for future taxonomic work. Wood deployments in a broad geographic range provided a powerful tool for research on Xylophagaidae allowing for conclusions on ecological requirements of xylophagaid species.Peer reviewe

Corrigendum: Wooden Stepping Stones: Diversity and Biogeography of Deep-Sea Wood Boring Xylophagaidae (Mollusca: Bivalvia) in the North-East Atlantic Ocean, With the Description of a New Genus

Peer reviewe

Map of sampling sites and wood with <i>Xylophaga</i> burrows.

<p>Map showing the position of the experimental moorings in relation to the Blanes Canyon (BC) and its outer slope (OS), drawn using GeoMapApp (<a href="http://www.geomapapp.org" target="_blank">http://www.geomapapp.org</a>). Insert, cube of pine wood (8 X 8 X 8 cm) colonized by <i>Xylophaga</i> after 12 months of immersion in Blanes Canyon.</p

Overview of the different samples in the whole experiment.

<p>Details on the locations of the traps used for pine and oak (Fagervold et al 2013) wood immersion experiments, as well as the samples taken from each trap. Abbreviations Bla 1.2, Bla 10, Bla 11 and Bla 1.1 refer to gills extractions from four <i>Xylophaga</i> sp. A individuals.</p><p>* =  Samples from Fagervold et al (2013) that were also used in this study.</p

Distribution of bacterial taxa.

<p>Relative proportion of the most abundant bacterial phylum or class (>1% of the sequences) found in wood, pellet and gill (Bla) samples from Blanes Canyon (BC) and its adjacent open slope (OS). *  =  contained significantly less sequences than the rest of the samples (n = 263).</p

Venn diagram representing bacterial OTUs unique and common to the wood samples, the pellet and the <i>Xylophaga</i> gills.

<p>Venn diagram representing bacterial OTUs unique and common to the wood samples, the pellet and the <i>Xylophaga</i> gills.</p

OTU network.

<p>Network showing associations between OTUs found in wood and pellets from wood immerged at various depths in Blanes Canyon (BC) and its adjacent open slope (OS). OTUs are represented as nodes (white circles) in the network and the size of each node is proportional to the number of sequences contained in each OTU. Lines connect the nodes that are the most correlated (MIC values>0.5). The identifying numbers of the most abundant OTUs are written in the nodes. Colors highlight associations between the OTUs that most explain the differences between groups of samples (Oak pellet, Pine pellet, BC Pine wood and OS Pine wood). OTUs that best explain differences between samples were identified by a SIMPER analysis.</p