Evidence for the Role of Horizontal Transfer in Generating pVT1, a Large Mosaic Conjugative Plasmid from the Clam Pathogen, Vibrio tapetis

The marine bacterium Vibrio tapetis is the causative agent of the brown ring disease, which affects the clam Ruditapes philippinarum and causes heavy economic losses in North of Europe and in Eastern Asia. Further characterization of V. tapetis isolates showed that all the investigated strains harbored at least one large plasmid. We determined the sequence of the 82,266 bp plasmid pVT1 from the CECT4600T reference strain and analyzed its genetic content. pVT1 is a mosaic plasmid closely related to several conjugative plasmids isolated from Vibrio vulnificus strains and was shown to be itself conjugative in Vibrios. In addition, it contains DNA regions that have similarity with several other plasmids from marine bacteria (Vibrio sp., Shewanella sp., Listonella anguillarum and Photobacterium profundum). pVT1 contains a number of mobile elements, including twelve Insertion Sequences or inactivated IS genes and an RS1 phage element related to the CTXphi phage of V. cholerae. The genetic organization of pVT1 underscores an important role of horizontal gene transfer through conjugative plasmid shuffling and transposition events in the acquisition of new genetic resources and in generating the pVT1 modular organization. In addition, pVT1 presents a copy number of 9, relatively high for a conjugative plasmid, and appears to belong to a new type of replicon, which may be specific to Vibrionaceae and Shewanelleacae

Introduction: Human ecology in the Himalaya

Knowledge of human adaptation in the Himalayas has developed more slowly than that for other world mountain systems. At the same time, the opening of the region to research has focused attention toward description in a “natural history” mode until quite recently. Where these studies have addressed issues of adaptation they have tended to do so more as a heuristic tool rather than in terms of contributing to the development of adaptive perspectives from a uniquely Himalayan vantage point. The contributions to this special issue suggest some of Himalayan cultural ecology's new themes as it more directly assumes a truly processual approach that incorporates the individual and domestic dimensions of adaptation within historical and social contexts .Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/44482/1/10745_2004_Article_BF00889710.pd

Determining microbial functional groups by stable isotope probing in a thermophilic anaerobic solid waste digestor

Présentation poster au colloque ISME-11, International Symposium on Microbial Ecology, 20-25 August 2006, Vienna, Austri

Evidence of active methanogen communities in shallow sediments of the Sonora Margin cold seeps

In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic Archaea were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic Methanococcoides burtonii relatives and several new autotrophic Methanogenium lineages, confirming the cooccurrence of Methanosarcinales and Methanomicrobiales methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps

Early diagenesis in the sediments of the Congo deep-sea fan dominated by massive terrigenous deposits: Part III – Sulfate- and methane- based microbial processes

International audienceGeochemical profiles (SO42-, H2S, CH4, δ13CH4) and phylogenetic diversity of Archaea and Bacteria from two oceanographic cruises dedicated to the lobes sediments of the Congo deep-sea fan are presented in this paper. In this area, organic-rich turbidites reach 5000 m and allow the establishment of patchy cold-seep-like habitats including microbial mats, reduced sediments, and vesicomyid bivalves assemblages. These bivalves live in endosymbiosis with sulfur-oxidizing bacteria and use sulfides to perform chemosynthesis. In these habitats, unlike classical abyssal sediments, anoxic processes are dominant. Total oxygen uptake fluxes and methane fluxes measured with benthic chambers are in the same range as those of active cold-seep environments, and oxygen is mainly used for reoxidation of reduced compounds, especially in bacterial mats and reduced sediments. High concentrations of methane and sulfate co-exist in the upper 20 cm of sediments, and evidence indicates that sulfate-reducing microorganisms and methanogens co-occur in the shallow layers of these sediments. Simultaneously, anaerobic oxidation of methane (AOM) with sulfate as the electron acceptor is evidenced by the presence of ANMEs (ANaerobic MEthanotroph). Dissolved sulfide produced through the reduction of sulfate is reoxidized through several pathways depending on the habitat. These pathways include vesicomyid bivalves uptake (adults or juveniles in the bacterial mats habitats), reoxidation by oxygen or iron phases within the reduced sediment, or reoxidation by microbial mats

Shape transition during nest digging in ants

Nest building in social insects is among the collective processes that show highly conservative features such as basic modules (chambers and galleries) or homeostatic properties. Although ant nests share common characteristics, they exhibit a high structural variability, of which morphogenesis and underlying mechanisms remain largely unknown. We conducted two-dimensional nest-digging experiments under homogeneous laboratory conditions to investigate the shape diversity that emerges only from digging dynamics and without the influence of any environmental heterogeneity. These experiments revealed that, during the excavation, a morphological transition occurs because the primary circular cavity evolves into a ramified structure through a branching process. Such a transition is observed, whatever the number of ants involved, but occurs more frequently for a larger number of workers. A stochastic model highlights the central role of density effects in shape transition. These results indicate that nest digging shares similar properties with various physical, chemical, and biological systems. Moreover, our model of morphogenesis provides an explanatory framework for shape transitions in decentralized growing structures in group-living animals