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Search Results: 1 - 10 of 196 matches for " Alban Ramette "
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Effects of Eutrophication, Seasonality and Macrofouling on the Diversity of Bacterial Biofilms in Equatorial Coral Reefs
Yvonne Sawall, Claudio Richter, Alban Ramette
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0039951
Abstract: Biofilms play an important role as a settlement cue for invertebrate larvae and significantly contribute to the nutrient turnover in aquatic ecosystems. Nevertheless, little is known about how biofilm community structure generally responds to environmental changes. This study aimed to identify patterns of bacterial dynamics in coral reef biofilms in response to associated macrofouling community structure, microhabitat (exposed vs. sheltered), seasonality, and eutrophication. Settlement tiles were deployed at four reefs along a cross-shelf eutrophication gradient and were exchanged every 4 months over 20 months. The fouling community composition on the tiles was recorded and the bacterial community structure was assessed with the community fingerprinting technique Automated Ribosomal Intergenic Spacer Analysis (ARISA). Bacterial operational taxonomic unit (OTU) number was higher on exposed tiles, where the fouling community was homogenous and algae-dominated, than in sheltered habitats, which were occupied by a variety of filter feeders. Furthermore, OTU number was also highest in eutrophied near-shore reefs, while seasonal variations in community structure were most pronounced in the oligotrophic mid-shelf reef. In contrast, the macrofouling community structure did not change significantly with seasons. Changes in bacterial community patterns were mostly affected by microhabitat, seasonal and anthropogenically derived changes in nutrient availability, and to a lesser extent by changes in the macrofouling community structure. Path analysis revealed a complex interplay of various environmental and biological factors explaining the spatial and temporal variations in bacterial biofilm communities under natural conditions.
Repeatedly Evolved Host-Specific Ectosymbioses between Sulfur-Oxidizing Bacteria and Amphipods Living in a Cave Ecosystem
Jan Bauermeister, Alban Ramette, Sharmishtha Dattagupta
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0050254
Abstract: Ectosymbioses between invertebrates and sulfur-oxidizing bacteria are widespread in sulfidic marine environments and have evolved independently in several invertebrate phyla. The first example from a freshwater habitat, involving Niphargus ictus amphipods and filamentous Thiothrix ectosymbionts, was recently reported from the sulfide-rich Frasassi caves in Italy. Subsequently, two new Niphargus species, N. frasassianus and N. montanarius, were discovered within Frasassi and found to co-occur with N. ictus. Using a variety of microscopic and molecular techniques, we found that all three Frasassi-dwelling Niphargus species harbor Thiothrix ectosymbionts, which belong to three distinct phylogenetic clades (named T1, T2, and T3). T1 and T3 Thiothrix dominate the N. frasassianus ectosymbiont community, whereas T2 and T3 are prevalent on N. ictus and N. montanarius. Relative distribution patterns of the three ectosymbionts are host species-specific and consistent over different sampling locations and collection years. Free-living counterparts of T1–T3 are rare or absent in Frasassi cave microbial mats, suggesting that ectosymbiont transmission among Niphargus occurs primarily through inter- or intraspecific inoculations. Phylogenetic analyses indicate that the Niphargus-Thiothrix association has evolved independently at least two times. While ectosymbioses with T1 and T2 may have been established within Frasassi, T3 ectosymbionts seem to have been introduced to the cave system by Niphargus.
Biogeography of Deep-Sea Benthic Bacteria at Regional Scale (LTER HAUSGARTEN, Fram Strait, Arctic)
Marianne Jacob, Thomas Soltwedel, Antje Boetius, Alban Ramette
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0072779
Abstract: Knowledge on spatial scales of the distribution of deep-sea life is still sparse, but highly relevant to the understanding of dispersal, habitat ranges and ecological processes. We examined regional spatial distribution patterns of the benthic bacterial community and covarying environmental parameters such as water depth, biomass and energy availability at the Arctic Long-Term Ecological Research (LTER) site HAUSGARTEN (Eastern Fram Strait). Samples from 13 stations were retrieved from a bathymetric (1,284–3,535 m water depth, 54 km in length) and a latitudinal transect (~ 2,500 m water depth; 123 km in length). 454 massively parallel tag sequencing (MPTS) and automated ribosomal intergenic spacer analysis (ARISA) were combined to describe both abundant and rare types shaping the bacterial community. This spatial sampling scheme allowed detection of up to 99% of the estimated richness on phylum and class levels. At the resolution of operational taxonomic units (97% sequence identity; OTU3%) only 36% of the Chao1 estimated richness was recovered, indicating a high diversity, mostly due to rare types (62% of all OTU3%). Accordingly, a high turnover of the bacterial community was also observed between any two sampling stations (average replacement of 79% of OTU3%), yet no direct correlation with spatial distance was observed within the region. Bacterial community composition and structure differed significantly with increasing water depth along the bathymetric transect. The relative sequence abundance of Verrucomicrobia and Planctomycetes decreased significantly with water depth, and that of Deferribacteres increased. Energy availability, estimated from phytodetrital pigment concentrations in the sediments, partly explained the variation in community structure. Overall, this study indicates a high proportion of unique bacterial types on relatively small spatial scales (tens of kilometers), and supports the sampling design of the LTER site HAUSGARTEN to study bacterial community shifts in this rapidly changing area of the world’s oceans.
Spatial Scales of Bacterial Diversity in Cold-Water Coral Reef Ecosystems
Sandra Sch?ttner, Christian Wild, Friederike Hoffmann, Antje Boetius, Alban Ramette
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0032093
Abstract: Background Cold-water coral reef ecosystems are recognized as biodiversity hotspots in the deep sea, but insights into their associated bacterial communities are still limited. Deciphering principle patterns of bacterial community variation over multiple spatial scales may however prove critical for a better understanding of factors contributing to cold-water coral reef stability and functioning. Methodology/Principal Findings Bacterial community structure, as determined by Automated Ribosomal Intergenic Spacer Analysis (ARISA), was investigated with respect to (i) microbial habitat type and (ii) coral species and color, as well as the three spatial components (iii) geomorphologic reef zoning, (iv) reef boundary, and (v) reef location. Communities revealed fundamental differences between coral-generated (branch surface, mucus) and ambient microbial habitats (seawater, sediments). This habitat specificity appeared pivotal for determining bacterial community shifts over all other study levels investigated. Coral-derived surfaces showed species-specific patterns, differing significantly between Lophelia pertusa and Madrepora oculata, but not between L. pertusa color types. Within the reef center, no community distinction corresponded to geomorphologic reef zoning for both coral-generated and ambient microbial habitats. Beyond the reef center, however, bacterial communities varied considerably from local to regional scales, with marked shifts toward the reef periphery as well as between different in- and offshore reef sites, suggesting significant biogeographic imprinting but weak microbe-host specificity. Conclusions/Significance This study presents the first multi-scale survey of bacterial diversity in cold-water coral reefs, spanning a total of five observational levels including three spatial scales. It demonstrates that bacterial communities in cold-water coral reefs are structured by multiple factors acting at different spatial scales, which has fundamental implications for the monitoring of microbial diversity and function in those ecosystems.
Quantifying the effect of environment stability on the transcription factor repertoire of marine microbes
Ivaylo Kostadinov, Renzo Kottmann, Alban Ramette, Jost Waldmann, Pier Luigi Buttigieg, Frank Gl?ckner
Microbial Informatics and Experimentation , 2011, DOI: 10.1186/2042-5783-1-9
Abstract: We quantified the effect of environment stability on the transcription factor repertoire of marine pelagic microbes from the Global Ocean Sampling (GOS) metagenome using interpolated physico-chemical parameters and multivariate statistics. Thirty-five percent of the difference in relative TF abundances between samples could be explained by environment stability. Six percent was attributable to spatial distance but none to a combination of both spatial distance and stability. Some individual TFs showed a stronger relationship to environment stability and space than the total TF pool.Environmental stability appears to have a clearly detectable effect on TF gene content in bacterioplanktonic communities described by the GOS metagenome. Interpolated environmental parameters were shown to compare well to in situ measurements and were essential for quantifying the effect of the environment on the TF content. It is demonstrated that comprehensive and well-structured contextual data will strongly enhance our ability to interpret the functional potential of microbes from metagenomic data.Microorganisms constantly adapt to their environment to survive. An efficient response mechanism is the regulation of transcription, the first step in gene expression, according to environmental demands. Transcription factors (TFs) are the primary agents that perform transcriptional regulation [1]. They consist of a DNA-binding domain (DBD) that typically targets regulatory elements upstream of a gene and an effector domain [2]. The majority of TFs operate by influencing the downstream transcription process and can be classified into 10 super-families according to their DNA-binding mechanisms [3]. Based on the number of genes they regulate, TFs can be divided into 'global regulators' and 'fine tuners' [4]. Both types exert targeted control over gene expression. Global regulators affect a larger number of genes from diverse metabolic pathways and respond to a wider set of stimuli [4,5]. Conve
Microbial Communities of Deep-Sea Methane Seeps at Hikurangi Continental Margin (New Zealand)
S. Emil Ruff, Julia Arnds, Katrin Knittel, Rudolf Amann, Gunter Wegener, Alban Ramette, Antje Boetius
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0072627
Abstract: The methane-emitting cold seeps of Hikurangi margin (New Zealand) are among the few deep-sea chemosynthetic ecosystems of the Southern Hemisphere known to date. Here we compared the biogeochemistry and microbial communities of a variety of Hikurangi cold seep ecosystems. These included highly reduced seep habitats dominated by bacterial mats, partially oxidized habitats populated by heterotrophic ampharetid polychaetes and deeply oxidized habitats dominated by chemosynthetic frenulate tubeworms. The ampharetid habitats were characterized by a thick oxic sediment layer that hosted a diverse and biomass-rich community of aerobic methanotrophic Gammaproteobacteria. These bacteria consumed up to 25% of the emanating methane and clustered within three deep-branching groups named Marine Methylotrophic Group (MMG) 1-3. MMG1 and MMG2 methylotrophs belong to the order Methylococcales, whereas MMG3 methylotrophs are related to the Methylophaga. Organisms of the groups MMG1 and MMG3 are close relatives of chemosynthetic endosymbionts of marine invertebrates. The anoxic sediment layers of all investigated seeps were dominated by anaerobic methanotrophic archaea (ANME) of the ANME-2 clade and sulfate-reducing Deltaproteobacteria. Microbial community analysis using Automated Ribosomal Intergenic Spacer Analysis (ARISA) showed that the different seep habitats hosted distinct microbial communities, which were strongly influenced by the seep-associated fauna and the geographic location. Despite outstanding features of Hikurangi seep communities, the organisms responsible for key ecosystem functions were similar to those found at seeps worldwide. This suggests that similar types of biogeochemical settings select for similar community composition regardless of geographic distance. Because ampharetid polychaetes are widespread at cold seeps the role of aerobic methanotrophy may have been underestimated in seafloor methane budgets.
Relationships between Host Phylogeny, Host Type and Bacterial Community Diversity in Cold-Water Coral Reef Sponges
Sandra Sch?ttner, Friederike Hoffmann, Paco Cárdenas, Hans Tore Rapp, Antje Boetius, Alban Ramette
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0055505
Abstract: Cold-water coral reefs are known to locally enhance the diversity of deep-sea fauna as well as of microbes. Sponges are among the most diverse faunal groups in these ecosystems, and many of them host large abundances of microbes in their tissues. In this study, twelve sponge species from three cold-water coral reefs off Norway were investigated for the relationship between sponge phylogenetic classification (species and family level), as well as sponge type (high versus low microbial abundance), and the diversity of sponge-associated bacterial communities, taking also geographic location and water depth into account. Community analysis by Automated Ribosomal Intergenic Spacer Analysis (ARISA) showed that as many as 345 (79%) of the 437 different bacterial operational taxonomic units (OTUs) detected in the dataset were shared between sponges and sediments, while only 70 (16%) appeared purely sponge-associated. Furthermore, changes in bacterial community structure were significantly related to sponge species (63% of explained community variation), sponge family (52%) or sponge type (30%), whereas mesoscale geographic distances and water depth showed comparatively small effects (<5% each). In addition, a highly significant, positive relationship between bacterial community dissimilarity and sponge phylogenetic distance was observed within the ancient family of the Geodiidae. Overall, the high diversity of sponges in cold-water coral reefs, combined with the observed sponge-related variation in bacterial community structure, support the idea that sponges represent heterogeneous, yet structured microbial habitats that contribute significantly to enhancing bacterial diversity in deep-sea ecosystems.
Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems
Lucie Zinger, Linda A. Amaral-Zettler, Jed A. Fuhrman, M. Claire Horner-Devine, Susan M. Huse, David B. Mark Welch, Jennifer B. H. Martiny, Mitchell Sogin, Antje Boetius, Alban Ramette
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0024570
Abstract: Background Marine microbial communities have been essential contributors to global biomass, nutrient cycling, and biodiversity since the early history of Earth, but so far their community distribution patterns remain unknown in most marine ecosystems. Methodology/Principal Findings The synthesis of 9.6 million bacterial V6-rRNA amplicons for 509 samples that span the global ocean's surface to the deep-sea floor shows that pelagic and benthic communities greatly differ, at all taxonomic levels, and share <10% bacterial types defined at 3% sequence similarity level. Surface and deep water, coastal and open ocean, and anoxic and oxic ecosystems host distinct communities that reflect productivity, land influences and other environmental constraints such as oxygen availability. The high variability of bacterial community composition specific to vent and coastal ecosystems reflects the heterogeneity and dynamic nature of these habitats. Both pelagic and benthic bacterial community distributions correlate with surface water productivity, reflecting the coupling between both realms by particle export. Also, differences in physical mixing may play a fundamental role in the distribution patterns of marine bacteria, as benthic communities showed a higher dissimilarity with increasing distance than pelagic communities. Conclusions/Significance This first synthesis of global bacterial distribution across different ecosystems of the World's oceans shows remarkable horizontal and vertical large-scale patterns in bacterial communities. This opens interesting perspectives for the definition of biogeographical biomes for bacteria of ocean waters and the seabed.
Microbial and Chemical Characterization of Underwater Fresh Water Springs in the Dead Sea
Danny Ionescu, Christian Siebert, Lubos Polerecky, Yaniv Y. Munwes, Christian Lott, Stefan H?usler, Mina Bi?i?-Ionescu, Christian Quast, J?rg Peplies, Frank Oliver Gl?ckner, Alban Ramette, Tino R?diger, Thorsten Dittmar, Aharon Oren, Stefan Geyer, Hans-Joachim St?rk, Martin Sauter, Tobias Licha, Jonathan B. Laronne, Dirk de Beer
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0038319
Abstract: Due to its extreme salinity and high Mg concentration the Dead Sea is characterized by a very low density of cells most of which are Archaea. We discovered several underwater fresh to brackish water springs in the Dead Sea harboring dense microbial communities. We provide the first characterization of these communities, discuss their possible origin, hydrochemical environment, energetic resources and the putative biogeochemical pathways they are mediating. Pyrosequencing of the 16S rRNA gene and community fingerprinting methods showed that the spring community originates from the Dead Sea sediments and not from the aquifer. Furthermore, it suggested that there is a dense Archaeal community in the shoreline pore water of the lake. Sequences of bacterial sulfate reducers, nitrifiers iron oxidizers and iron reducers were identified as well. Analysis of white and green biofilms suggested that sulfide oxidation through chemolitotrophy and phototrophy is highly significant. Hyperspectral analysis showed a tight association between abundant green sulfur bacteria and cyanobacteria in the green biofilms. Together, our findings show that the Dead Sea floor harbors diverse microbial communities, part of which is not known from other hypersaline environments. Analysis of the water’s chemistry shows evidence of microbial activity along the path and suggests that the springs supply nitrogen, phosphorus and organic matter to the microbial communities in the Dead Sea. The underwater springs are a newly recognized water source for the Dead Sea. Their input of microorganisms and nutrients needs to be considered in the assessment of possible impact of dilution events of the lake surface waters, such as those that will occur in the future due to the intended establishment of the Red Sea?Dead Sea water conduit.
Combinaison d'informations géographiques en mode image: application à l'estuaire de la Seine
Alban BOURCIER
Mappemonde , 1993,
Abstract: En présentant une série de traitements visant la combinaison et la représentation cartographique d’informations géographiques, l’objectif est de promouvoir la gestion d’informations à caractère spatial en mode image.
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