Melitea salexigens gen. nov., sp. nov., a gammaproteobacterium from the Mediterranean Sea

International audienceA 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 mm long and 0.5 mm 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)

Structures of benthic prokaryotic communities and their hydrolytic enzyme activities resuspended from samples of intertidal mudflats: An experimental approach

International audienceResuspended sediment can increase plankton biomass and the growth of bacteria, thus influencing the coastal planktonic microbial food web. But little is known about resuspension itself: is it a single massive change or a whole series of events and how does it affect the quantity and quality of resuspended prokaryotic cells? We simulated the sequential erosion of mud cores to better understand the fate and role of benthic prokaryotes resus-pended in the water column. We analyzed the total, attached and free-living prokaryotic cells resuspended, their structure and the activities of their hydrolytic enzymes in terms of the biotic and abiotic factors that affect the composition of microphytobenthic biofilm. Free living prokaryotes were resuspended during the fluff layer erosion phase (for shear velocities below 5 cm · s −1) regardless of the bed sediment composition. At the higher shear velocities, resuspended prokaryotes were attached to particulate matter. Free and attached cells are thus unevenly distributed, scattered throughout the organic matter (OM) in the uppermost mm of the sediment. Only 10–27% of the total cells initially resuspended were living and most of the Bacteria were Cyanobacteria and Gamma-proteobacteria; their numbers increased to over 30% in parallel with the hydrolytic enzyme activity at highest shear velocity. These conditions released prokaryotic cells having different functions that lie deep in the sediment; the most important of them are Archaea. Finally, composition of resuspended bacterial populations varied with resuspension intensity, and intense resus-pension events boosted the microbial dynamics and enzyme activities in the bottom layers of sea water

Temporal Dynamics of Active Prokaryotic Nitrifiers and Archaeal Communities from River to Sea

International audienceTo test if different niches for potential nitrifiers exist in estuarine systems, we assessed by pyrosequencing the diversity of archaeal gene transcript markers for taxonomy (16S ribosomal RNA (rRNA)) during an entire year along a salinity gradient in surface waters of the Charente estuary (Atlantic coast, France). We further investigated the potential for estuarine prokaryotes to oxidize ammonia and hydrolyze urea by quantifying thaumarchaeal amoA and ureC and bacterial amoA transcripts. Our results showed a succession of different nitrifiers from river to sea with bacterial amoA transcripts dominating in the freshwater station while archaeal transcripts were predominant in the marine station. The 16S rRNA sequence analysis revealed that Thaumarchaeota marine group I (MGI) were the most abundant overall but other archaeal groups like Methanosaeta were also potentially active in winter (December–March) and Euryarchaeota marine group II (MGII) were dominant in seawater in summer (April–August). Each station also contained different Thaumarchaeota MGI phylogenetic clusters, and the clusters' microdiversity was associated to specific environmental conditions suggesting the presence of ecotypes adapted to distinct ecological niches. The amoA and ureC transcript dynamics further indicated that some of the Thaumarchaeota MGI sub-clusters were involved in ammonia oxidation through the hy-drolysis of urea. Our findings show that ammonia-oxidizing Archaea and Bacteria were adapted to contrasted conditions and that the Thaumarchaeota MGI diversity probably corresponds to distinct metabolisms or life strategies

Low-abundant but highly transcriptionally active uncharacterised Nitrosomonas drive ammonia-oxidation in the Brouage mudflat, France

Exploring differences in nitrification within adjacent sedimentary structures of ridges and runnels on the Brouage mudflat, France, we quantified Potential Nitrification Rates (PNR) alongside amoA genes and transcripts. PNR was lower in ridges (≈1.7 fold-lower) than runnels, despite higher (≈1.8 fold-higher) ammonia-oxidizing bacteria (AOB) abundance. However, AOB were more transcriptionally active in runnels (≈1.9 fold-higher). Sequencing of amoA genes and transcripts revealed starkly contrasting profiles with transcripts from ridges and runnels dominated (≈91 % in ridges and ≈98 % in runnels) by low abundant (≈4.6 % of the DNA community in runnels and ≈0.8 % in ridges) but highly active phylotypes. The higher PNR in runnels was explained by higher abundance of this group, an uncharacterised Nitrosomonas sp. cluster. This cluster is phylogenetically similar to other active ammonia-oxidizers with worldwide distribution in coastal environments indicating its potential, but previously overlooked, contribution to ammonia oxidation globally. In contrast DNA profiles were dominated by highly abundant but low-activity clusters phylogenetically distinct from known Nitrosomonas (Nm) and Nitrosospira (Ns). This cluster is also globally distributed in coastal sediments, primarily detected as DNA, and often classified as Nitrosospira or Nitrosomonas. We therefore propose to classify this cluster as Ns/Nm. Our work indicates that low abundant but highly active AOB could be responsible for the nitrification globally, while the abundant AOB Ns/Nm may not be transcriptionally active, and as such account for the lack of correlation between rate processes and gene abundances often reported in the literature. It also raises the question as to what this seemingly inactive group is doing

Very Low Phytoplankton Diversity in a Tropical Saline-Alkaline Lake, with Co-dominance of Arthrospira fusiformis (Cyanobacteria) and Picocystis salinarum (Chlorophyta)

International audienceLake Dziani Dzaha (Mayotte Island, Indian Ocean) is a tropical thalassohaline lake which geochemical and biological conditions make it a unique aquatic ecosystem considered as a modern analogue of Precambrian environments. In the present study, we focused on the diversity of phytoplanktonic communities, which produce very high and stable biomass (mean 2014-2015 = 652 ± 179 μg chlorophyll a L −1). As predicted by classical community ecology paradigms, and as observed in similar environments, a single species is expected to dominate the phytoplanktonic communities. To test this hypothesis, we sampled water column in the deepest part of the lake (18 m) during rainy and dry seasons for two consecutive years. Phytoplanktonic communities were characterized using a combination of metagenomic, microscopy-based and flow cytometry approaches, and we used statistical modeling to identify the environmental factors determining the abundance of dominant organisms. As hypothesized, the overall diversity of the phytoplanktonic communities was very low (15 OTUs), but we observed a co-dominance of two, and not only one, OTUs, viz., Arthrospira fusiformis (Cyanobacteria) and Picocystis salinarum (Chlorophyta). We observed a decrease in the abundance of these co-dominant taxa along the depth profile and identified the adverse environmental factors driving this decline. The functional traits measured on isolated strains of these two taxa (i.e., size, pigment composition, and concentration) are then compared and discussed to explain their capacity to cope with the extreme environmental conditions encountered in the aphotic, anoxic, and sulfidic layers of the water column of Lake Dziani Dzaha

Diversité des bactéries de la microcouche de surface de l’eau de mer : spécificité, adaptation et résistance aux radiations solaires

The sea surface microlayer (first mm of the sea surface), located at the air-water interface, is often enriched in organic matter originating from natural and anthropogenic sources from the atmosphere, from freshwater inputs and from biological activities of the natural ecosystem. This enrichment in organic matter allows a high biological activity and the abundance of microorganisms, named the bacterioneuston, is generally higher when compared to underlying waters. A large number of samplers or sampling techniques have being designed for collection of the first (m of the sea surface microlayer. Initially, we made an methodological study in order to determine the most suitable method of sampling the biological communities of the sea surface microlayer. During several field campaigns on two coastal sites of the north-western Mediterranean Sea, sea surface microlayer and underlying waters samples were collected to isolate culturable bacteria and their diversity was characterized. A collection of 125 isolates was made. The sequencing of the 16S rRNA gene of each isolates revealed a large diversity amongst the bacteria isolated from the sea surface microlayer. Based on phylogenetic analyses, bacterial communities from the sea surface microlayer were similar to those from underlying waters. Amongst the bacteria isolated, several were only distantly related to known species. Lastly, bacterial isolates were screened for resistance to simulated solar radiation. The majority of the isolates were resistant to simulated solar radiation, independent of their origin in the water column. These results provide important information concerning the diversity and adaptation strategies of bacterioneuston to the extreme environment of the sea surface microlayer.La microcouche de surface (premier mm de la surface des océans), située à l’interface entre l’air et l’eau, est souvent enrichie en matières organiques d’origine naturelle et anthropique issues des apports fluviatiles et atmosphériques et de l’activité biologique du milieu naturel. Cette richesse enmatières organiques permet une forte activité biologique et la densité des microorganismes, qui constituent le bactérioneuston, est souvent très supérieure à celle trouvée dans la colonne d’eau. De nombreuses méthodes d’échantillonnage sont disponibles pour collecter les premiers (m de la surfacedes océans. Dans un premier temps, une étude méthodologique a été menée afin de mettre en évidence le ou les échantillonneur(s) le(s) plus approprié(s) pour étudier les communautés biologiques présentes à cette interface. Lors de plusieurs campagnes de prélèvements sur deux sites côtiers du nord-ouest de la mer Méditerranée, des échantillons de microcouche de surface et d’eau sous-jacente ont été collectés pour isoler et analyser la diversité des bactéries cultivables. Une collection de 125 souches a été constituée. Le séquençage de l’ADNr 16S a révélé une grande diversité parmi les bactéries isolées de la microcouche. Ces communautés bactériennes n’étaient pas très différentes sur un plan phylogénétique de celles opérant dans la colonne d’eau. Parmi les souches isolées, certaines étaient très éloignées taxonomiquement d’espèces connues. Dans un dernier temps, la résistance des souches de la collection face aux radiation solaires a été évaluée grâce à l’utilisation d’un simulateur solaire. Une majorité des souches a présenté une résistance importante face aux radiations solaires et ceci quelque soit leur localisation dans la colonne d’eau. L’ensemble des données obtenues nous a apporté des informations concernant la diversité et les stratégies d’adaptation du bactérioneuston à l’environnement particulier de la microcouche de surface