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ABSTRACT: Bacterial assemblages from subsurface (100 m depth), meso- (200-1000 m depth) and bathy-pelagic (below 1000 m depth) zones at 10 stations along a North Atlantic Ocean transect from 60°N to 5°S were characterized using massively parallel pyrotag sequencing of the V6 region of the 16S rRNA gene (V6 pyrotags). In a dataset of more than 830,000 pyrotags, we identified 10,780 OTUs of which 52% were singletons. The singletons accounted for less than 2% of the OTU abundance, whereas the 100 and 1000 most abundant OTUs represented 80% and 96% respectively of all recovered OTUs. Non-metric Multi-Dimensional Scaling and Canonical Correspondence Analysis of all the OTUs excluding the singletons revealed a clear clustering of the bacterial communities according to the water masses. More than 80% of the 1000 most abundant OTUs corresponded to Proteobacteria of which 55% were Alphaproteobacteria, mostly composed of the SAR11 cluster. Gammaproteobacteria increased with depth and included a relatively large number of OTUs belonging to Alteromonadales and Oceanospirillales. The bathypelagic zone showed higher taxonomic evenness than the overlying waters, albeit bacterial diversity was remarkably variable. Both abundant and low-abundance OTUs were responsible for the distinct bacterial communities characterizing the major deep-water masses. Taken together, our results reveal that deep-water masses act as bio-oceanographic islands for bacterioplankton leading to water mass-specific bacterial communities in the deep waters of the Atlantic.
Molecular Ecology 01/2011; 20(2):258-74. · 5.52 Impact Factor
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ABSTRACT: A novel aerobic, Gram-negative bacterial strain, designated 5IX/A01/131(T), was isolated from waters in the coastal north-western Mediterranean Sea. The cells were motile, straight rods, 1.6 microm long and 0.5 microm wide, and formed cream colonies on marine 2216 agar. The G+C content of the genomic DNA was 57 mol %. Phylogenetic analysis of the 16S rRNA gene sequence placed the strain in the class Gammaproteobacteria. On the basis of the 16S rRNA gene sequence comparisons and physiological and biochemical characteristics, strain 5IX/A01/131(T) represents a novel genus and species, for which the name Melitea salexigens gen. nov., sp. nov. is proposed. The type strain of Melitea salexigens is 5IX/A01/131(T) (=DSM 19753(T) =CIP 109757(T) =MOLA 225(T)).
International journal of systematic and evolutionary microbiology 12/2008; 58(Pt 11):2479-83. · 2.27 Impact Factor
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ABSTRACT: Aerobic nitrification of ammonia to nitrite and nitrate is a key process in the oceanic nitrogen cycling mediated by prokaryotes. Apart from Bacteria belonging to the beta- and gamma-Proteobacteria involved in the first nitrification step, Crenarchaeota have recently been recognized as main drivers of the oxidation of ammonia to nitrite in soil as well as in the ocean, as indicated by the dominance of archaeal ammonia monooxygenase (amoA) genes over bacterial amoA. Evidence is accumulating that archaeal amoA genes are common in a wide range of marine systems. Essentially, all these reports focused on surface and mesopelagic (200-1,000 m depth) waters, where ammonia concentrations are higher than in waters below 1,000 m depth. However, Crenarchaeota are also abundant in the water column below 1,000 m, where ammonia concentrations are extremely low. Here we show that, throughout the North Atlantic Ocean, the abundance of archaeal amoA genes decreases markedly from subsurface waters to 4,000 m depth, and from subpolar to equatorial deep waters, leading to pronounced vertical and latitudinal gradients in the ratio of archaeal amoA to crenarchaeal 16S ribosomal RNA (rRNA) genes. The lack of significant copy numbers of amoA genes and the very low fixation rates of dark carbon dioxide in the bathypelagic North Atlantic suggest that most bathypelagic Crenarchaeota are not autotrophic ammonia oxidizers: most likely, they utilize organic matter and hence live heterotrophically.
Nature 12/2008; 456(7223):788-91. · 36.28 Impact Factor
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ABSTRACT: Until recently, ammonia oxidation, a key process in the global nitrogen cycle, was thought to be mediated exclusively by a few bacterial groups. It has been shown now, that also Crenarchaeota are capable to perform this initial nitrification step. The abundance of ammonia oxidizing Bacteria and Archaea was determined using the bacterial and archaeal ammonia monooxygenase-alpha subunit (amoA) gene as functional markers in a quantitative PCR approach and related to the abundance of Bacteria and Archaea in the Eastern Mediterranean Sea. Archaeal amoA copy numbers decreased from 4000-5000 copies ml(-1) seawater from the 200-500 m depth layer to 20 copies ml(-1) at 1000 m depth. Beta-proteobacterial amoA genes were below the detection limit in all the samples. The archaeal amoA copy numbers were correlated with NO(2)(-) concentrations, suggesting that ammonia-oxidizing Archaea may play a significant role in the nitrification in the mesopelagic waters of the Eastern Mediterranean Sea. In the bathypelagic waters, however, archaeal amoA gene abundance was rather low although Crenarchaeota were abundant, indicating that Crenarchaeota might largely lack the amoA gene in these deep waters. Terminal restriction fragment length polymorphism analysis of the archaeal community revealed a distinct clustering with the mesopelagic community distinctly different from the archaeal communities of both, the surface waters and the 3000-4000 m layers. Hence, the archaeal community in the Eastern Mediterranean Sea appears to be highly stratified despite the absence of major temperature and density gradients between the meso- and bathypelagic waters of the Mediterranean Sea.
The ISME Journal 10/2008; 3(2):147-58. · 7.38 Impact Factor
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ABSTRACT: A novel aerobic, Gram-negative bacterium, named 13IX/A01/164(T), was isolated from surface waters in the coastal north-western Mediterranean Sea. Cells were motile, straight rods, 2.5 mum long and 0.2 mum wide, and formed orange colonies on marine agar medium. The G+C content of the genomic DNA of strain 13IX/A01/164(T) was 42 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed the strain in the phylum Bacteroidetes within the family Crenotrichaceae. On the basis of 16S rRNA gene sequence comparison and physiological and biochemical characteristics, this isolate represents a novel species of a new genus, for which the name Balneola vulgaris gen. nov., sp. nov. is proposed. The type strain of Balneola vulgaris is 13IX/A01/164(T) (=DSM 17893(T)=CIP 109092(T)=OOB 256(T)).
International journal of systematic and evolutionary microbiology 09/2006; 56(Pt 8):1883-7. · 2.27 Impact Factor
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ABSTRACT: Bacterial populations inhabiting the sea surface microlayer from two contrasted Mediterranean coastal stations (polluted vs. oligotrophic) were examined by culturing and genetic fingerprinting methods and were compared with those of underlying waters (50 cm depth), for a period of two years. More than 30 samples were examined and 487 strains were isolated and screened. Proteobacteria were consistently more abundant in the collection from the pristine environment whereas Gram-positive bacteria (i.e., Actinobacteria and Firmicutes) were more abundant in the polluted site. Cythophaga-Flavobacter-Bacteroides (CFB) ranged from 8% to 16% of total strains. Overall, 22.5% of the strains showed a 16S rRNA gene sequence similarity only at the genus level with previously reported bacterial species and around 10.5% of the strains showed similarities in 16S rRNA sequence below 93% with reported species. The CFB group contained the highest proportion of unknown species, but these also included Alpha- and Gammaproteobacteria. Such low similarity values showed that we were able to culture new marine genera and possibly new families, indicating that the sea-surface layer is a poorly understood microbial environment and may represent a natural source of new microorganisms. Genetic fingerprinting showed, however, no consistent differences between the predominant bacterial assemblages from surface microlayer and underlying waters, suggesting that the presence of a stable and abundant neustonic bacterial community is not a common trait of coastal marine environments.
FEMS Microbiology Ecology 11/2005; 54(2):269-80. · 3.41 Impact Factor
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ABSTRACT: A total of 90 bacterial strains were isolated from the sea surface microlayer (i.e., bacterioneuston) and underlying waters (i.e., bacterioplankton) from two sites of the northwestern Mediterranean Sea. The strains were identified by sequence analysis, and growth recovery was investigated after exposure to simulated solar radiation. Bacterioneuston and bacterioplankton isolates were subjected to six different exposure times, ranging from 0.5 to 7 h of simulated noontime solar radiation. Following exposure, the growth of each isolate was monitored, and different classes of resistance were determined according to the growth pattern. Large interspecific differences among the 90 marine isolates were observed. Medium and highly resistant strains accounted for 41% and 22% of the isolates, respectively, and only 16% were sensitive strains. Resistance to solar radiation was equally distributed within the bacterioneuston and bacterioplankton. Relative contributions to the highly resistant class were 43% for gamma-proteobacteria and 14% and 8% for alpha-proteobacteria and the Cytophaga/Flavobacterium/Bacteroides (CFB) group, respectively. Within the gamma-proteobacteria, the Pseudoalteromonas and Alteromonas genera appeared to be highly resistant to solar radiation. The majority of the CFB group (76%) had medium resistance. Our study further provides evidence that pigmented bacteria are not more resistant to solar radiation than nonpigmented bacteria.
Applied and Environmental Microbiology 10/2005; 71(9):5282-9. · 3.83 Impact Factor
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Hélène Agogué,
Emilio O Casamayor,
Fabien Joux,
Ingrid Obernosterer,
Christine Dupuy,
François Lantoine,
Philippe Catala,
Markus G Weinbauer,
Thomas Reinthaler,
Gerhard J Herndl,
Philippe Lebaron
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ABSTRACT: The surface film of the hydrosphere covers more than 70% of the world’s surface. The sea surface microlayer (SML) or “skin” of the ocean is a sink for natural and anthropogenic material originating from the atmosphere and the water column. Organisms living in this SML are called “neuston.” Our knowledge of the biology of the SML is still in its infancy. Research of the sea surface microlayer requires the use of appropriate sampling techniques and strategies, and the question of what is the most suitable device has not yet been answered. In the present study, we have compared the efficiency of the Harvey glass plate (GP) and the Garrett metal screen (MS) to analyze a wide range of microbiological parameters in SML samples collected at two coastal stations in the NW Mediterranean Sea. Two types of membranes (Teflon and polycarbonate) were also used to collect bacterioneuston. The MS was the most appropriate technique for most biological parameters providing higher enrichment factors as compared to the GP and, therefore, the highest enrichment factors compared with underlying waters (UW). Control experiments with UW demonstrated that the enrichment reported for the MS was not biased by any selectivity of the sampler itself. Therefore, we recommend the use of the MS when the aim is to compare different biological parameters. In contrast, there is clear evidence that hydrophobic and hydrophilic membranes have an important drawback and should not be used for quantification purposes.
Limnology and oceanography, methods 01/2004; 2:213-225. · 1.53 Impact Factor
