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Durand, J. D., Shen, K. N., Chen, W. J., Jamandre, B. W., Blel, H., Diop, K., et al. (2012). Systematics of the grey mullets (Teleostei: Mugiliformes: Mugilidae): Molecular phylogenetic evidence challenges two centuries of morphology-based taxonomy. Mol. Phylogenet. Evol., 64(1), 73–92.
Résumé: The family Mugilidae comprises mainly coastal marine species that a:e widely distributed in all tropical, subtropical and temperate seas. Mugilid species are generally considered to be ecologically important and they are a major food resource for human populations in certain parts of the world. The taxonomy and systematics of the Mugilidae are still much debated and based primarily on morphological characters. In this study, we provide the first comprehensive molecular systematic account of the Mugilidae using phylogenetic analyses of nucleotide sequence variation at three mitochondrial loci (16S rRNA, cytochrome oxidase 1, and cytochrome b) for 257 individuals from 55 currently recognized species. The study covers all 20 mugilid genera currently recognized as being valid. The family comprises seven major lineages that radiated early on from the ancestor to all current forms. All genera that were represented by two species or more, except Cestraeus, turned out to be paraphyletic or polyphyletic. Thus, the present phylogenetic results generally disagree with the current taxonomy at the genus level and imply that the anatomical characters used for the systematics of the Mugilidae may be poorly informative phylogenetically. The present results should provide a sound basis for a taxonomic revision of the mugilid genera. A proportion of the species with large distribution ranges (including Moolgarda seheli, Mugil cephalus and M. curema) appear to consist of cryptic species, thus warranting further taxonomic and genetic work at the infra-generic level. (c) 2012 Elsevier Inc. All rights reserved.
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Pereira, O., Hochart, C., Auguet, J. C., Debroas, D., & Galand, P. E. (2019). Genomic ecology of Marine Group II, the most common marine planktonic Archaea across the surface ocean. MicrobiologyOpen, 8(9), e852.
Résumé: Planktonic Archaea have been detected in all the world's oceans and are found from surface waters to the deep sea. The two most common Archaea phyla are Thaumarchaeota and Euryarchaeota. Euryarchaeota are generally more common in surface waters, but very little is known about their ecology and their potential metabolisms. In this study, we explore the genomic ecology of the Marine Group II (MGII), the main marine planktonic Euryarchaeota, and test if it is composed of different ecologically relevant units. We re-analyzed Tara Oceans metagenomes from the photic layer and the deep ocean by annotating sequences against a custom MGII database and by mapping gene co-occurrences. Our data provide a global view of the distribution of Euryarchaeota, and more specifically of MGII subgroups, and reveal their association to a number of gene-coding sequences. In particular, we show that MGII proteorhodopsins were detected in both the surface and the deep chlorophyll maximum layer and that different clusters of these light harvesting proteins were present. Our approach helped describing the set of genes found together with specific MGII subgroups. We could thus define genomic environments that could theoretically describe ecologically meaningful units and the ecological niche that they occupy.
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Vila-Costa, M., Barberan, A., Auguet, J. - C., Sharma, S., Moran, M. A., & Casamayor, E. O. (2013). Bacterial and archaeal community structure in the surface microlayer of high mountain lakes examined under two atmospheric aerosol loading scenarios. FEMS Microbiology Ecology, .
Résumé: Bacteria and Archaea of the air-water surface microlayer (neuston) and plankton from three high mountain lakes (Limnological Observatory of the Pyrenees, Spain) were analyzed by 16S rRNA gene 454 pyrosequencing (V6 region) in two dates with different atmospheric aerosol loading conditions: (i) under a Saharan dust plume driven by southern winds, and (ii) under northern winds with oceanic influence. In general, bacterial communities were richer than archaea, with estimated total richness of 2,500 OTUs for Bacteria and 900 OTUs for Archaea equivalent to a sequencing effort of 250,000 and 20,000 sequences, respectively. The dominant bacterial OTU was affiliated to Actinobacteria. Archaea were one to two orders-of-magnitude less abundant than bacteria but were more evenly distributed. Apparently, Bacteroidetes and Thaumarchaeota sequences were preferentially found at the neuston, but no consistent pattern in either total microbial abundance or richness was found in any sample. However, we observed more marked changes in microbial relative abundances between neuston and plankton in the dust-influenced scenario. Higher community dissimilarities between neuston and plankton were also found during the Saharan dust episode, and such differences were higher for Bacteria than for Archaea. Nonetheless, relatively few (<0.05%) of the neuston sequences matched previously identified airborne microbes, and none became important in the dates analyzed. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved
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