Predominant heterotrophic diazotrophic bacteria are involved in Sargassum proliferation in the Great Atlantic Sargassum Belt.

Since 2011, the Caribbean coasts have been subject to episodic influxes of floating Sargassum seaweed of unprecedented magnitude originating from a new area "the Great Atlantic Sargassum Belt" (GASB), leading in episodic influxes and mass strandings of floating Sargassum. For the biofilm of both holopelagic and benthic Sargassum as well as in the surrounding waters, we characterized the main functional groups involved in the microbial nitrogen cycle. The abundance of genes representing nitrogen fixation (nifH), nitrification (amoA), and denitrification (nosZ) showed the predominance of diazotrophs, particularly within the GASB and the Sargasso Sea.

In situ observations and modelling revealed environmental factors favouring occurrence of Vibrio in microbiome of the pelagic Sargassum responsible for strandings.

Historically, pelagic Sargassum were only found in the Sargasso Sea. Since 2011, blooms were regularly observed in warmer water, further south. Their developments in Central Atlantic are associated with mass strandings on the coasts, causing important damages and potentially dispersion of new bacteria.

Salinity shifts in marine sediment: Importance of number of fluctuation rather than their intensities on bacterial denitrifying community.

The sensitivity of denitrifying community to salinity fluctuations was studied in microcosms filled with marine coastal sediments subjected to different salinity disturbances over time (sediment under frequent salinity changes vs sediment with "stable" salinity pattern). Upon short-term salinity shift, denitrification rate and denitrifiers abundance showed high resistance whatever the sediment origin is. Denitrifying community adapted to frequent salinity changes showed high resistance when salinity increases, with a dynamic nosZ relative expression level.

The nature of the electron acceptor (MnIV/NO3) triggers the differential expression of genes associated with stress and ammonium limitation responses in Shewanella algae C6G3.

Shewanella algae C6G3 can dissimilatively reduce nitrate into ammonium and manganese oxide (MnIV) into MnII. It has the unusual ability to anaerobically produce nitrite from ammonium in the presence of MnIV. To gain insight into their metabolic capabilities, global mRNA expression patterns were investigated by RNA-seq and qRT-PCR in cells growing with lactate and ammonium as carbon and nitrogen sources, and with either MnIV or nitrate as electron acceptors.

Physiological and transcriptional approaches reveal connection between nitrogen and manganese cycles in Shewanella algae C6G3.

To explain anaerobic nitrite/nitrate production at the expense of ammonium mediated by manganese oxide (Mn(IV)) in sediment, nitrate and manganese respirations were investigated in a strain (Shewanella algae C6G3) presenting these features. In contrast to S. oneidensis MR-1, a biotic transitory nitrite accumulation at the expense of ammonium was observed in S.

Metatranscriptomes of oil-contaminated marine coastal sediment affected by oil addition and/or by the bioturbating activity of the marine polychaete Hediste diversicolor: Who are the microbial players?

In coastal marine sediment, oxygen fluctuations induced by bioturbating activities are widespread and exert a great influence, not only on the structure and diversity of the microbenthic communities, but also on their activities. Thus, the activity of benthic organisms can have a significant influence on the degradation of hydrocarbons (HC) and can favor the development of hydrocarbonoclastic microorganisms in contaminated marine sediments. Here, we have generated metatranscriptomic data from coastal marine sediments affected by oil addition and/or by the reworking activity of the marine polychaete Hediste diversicolor to gain insights into the active microbial groups involved in the response to oil addition under the oxygen-fluctuating conditions.

Draft-genome sequence of Shewanella algae strain C6G3.

Shewanella algae strain C6G3, isolated from the 2 uppermost centimeters of muddy sediment of Arcachon Bay (SW Atlantic French coast, sampled in October 2007) has the capability to use a large panel of terminal electron acceptors under anaerobic condition, such as nitrate, nitrite and metal-oxide, and presents a great metabolic versatility. Here, we present the non-contiguous draft-genome sequence of Shewanella algae C6G3, which consists of a 4,879,425 bp. The chromosome contains 5792 predicted genes.

Ecological significance of Synergistetes in the biological treatment of tuna cooking wastewater by an anaerobic sequencing batch reactor.

Lab-scale 2L-anaerobic sequencing batch reactor was operated under mesothermic conditions. The degradation of protein-rich organic matter was determined by chemical oxygen demand, biogas production, and protein-removal activity over the operation. The structure of the microbial community was determined by qPCR and next-generation sequencing on 16S rRNA genes.

Use of dispersant in mudflat oil-contaminated sediment: behavior and effects of dispersed oil on micro- and macrobenthos.

The present study aimed to examine whether the use of dispersant would be suitable for favoring the hydrocarbon degradation in coastal marine sediments without impacting negatively micro- and macrobenthic organisms. Mudflat sediments, maintained during 286 days in mesocosms designed to simulate natural conditions, were contaminated or not with Ural blend crude oil (REBCO) and treated or not with third-generation dispersant (Finasol OSR52). While the dispersant did not lead to an increase of hydrocarbon biodegradation, its use enables an attenuation of more than 55 % of the sediment concentration of total petroleum hydrocarbons (TPH).

Effect of physical sediments reworking on hydrocarbon degradation and bacterial community structure in marine coastal sediments.

The present study aimed to examine whether the physical reworking of sediments by harrowing would be suitable for favouring the hydrocarbon degradation in coastal marine sediments. Mudflat sediments were maintained in mesocosms under conditions as closer as possible to those prevailing in natural environments with tidal cycles. Sediments were contaminated with Ural blend crude oil, and in half of them, harrowing treatment was applied in order to mimic physical reworking of surface sediments.

Dynamic of bacterial communities attached to lightened phytodetritus.

The effects of singlet oxygen ((1)O2) transfer to bacteria attached on phytodetritus were investigated under laboratory-controlled conditions. For this purpose, a nonaxenic culture of Emiliania huxleyi in late stationary phase was studied for bacterial viability. Our results indicated that only 9 ± 3% of attached bacteria were alive compared to 46 ± 23% for free bacteria in the E.

Substrates specialization in lipid compounds and hydrocarbons of Marinobacter genus.

The impact of petroleum contamination and of burrowing macrofauna on abundances of Marinobacter and denitrifiers was tested in marine sediment mesocoms after 3 months incubation. Quantification of this genus by qPCR with a new primer set showed that the main factor favoring Marinobacter abundance was hydrocarbon amendment followed by macrofauna presence. In parallel, proportion of nosZ-harboring bacteria increased in the presence of marcrofauna.

Bacterial diversity in relatively pristine and anthropogenically-influenced mangrove ecosystems (Goa, India).

To appreciate differences in benthic bacterial community composition at the relatively pristine Tuvem and the anthropogenically-influenced Divar mangrove ecosystems in Goa, India, parallel tag sequencing of the V6 region of 16S rDNA was carried out. We hypothesize that availability of extraneously-derived anthropogenic substrates could act as a stimulatant but not a deterrent to promote higher bacterial diversity at Divar. Our observations revealed that the phylum Proteobacteria was dominant at both locations comprising 43-46% of total tags.

Trends in salinity and inorganic nitrogen compounds in the Berre lagoon (1994-2011) bacterial activities and nitrogen budgets.

The Berre lagoon receives freshwater from two natural rivers but the implementation of the hydroelectric power plant led to strong changes in the ecosystem structure and functioning. Sediments are important sites for nitrogen cycling because the O(2) sharp gradient allows oxic nitrification as well as anoxic denitrification and anammox to operate in close proximity. Seasonal and short-term variations in the coastal nitrogen processes were quantified at two stations: SA1 located in the northern part of the lagoon directly under the inflows of freshwater and SA3 in the southern part of the lagoon influenced mainly by the marine water inflows.

Genome sequence of the marine bacterium Marinobacter hydrocarbonoclasticus SP17, which forms biofilms on hydrophobic organic compounds.

Marinobacter hydrocarbonoclasticus SP17 forms biofilms specifically at the interface between water and hydrophobic organic compounds (HOCs) that are used as carbon and energy sources. Biofilm formation at the HOC-water interface has been recognized as a strategy to overcome the low availability of these nearly water-insoluble substrates. Here, we present the genome sequence of SP17, which could provide further insights into the mechanisms of enhancement of HOCs assimilation through biofilm formation.

Nitrogen-limited mangrove ecosystems conserve N through dissimilatory nitrate reduction to ammonium.

Earlier observations in mangrove sediments of Goa, India have shown denitrification to be a major pathway for N loss. However, percentage of total nitrate transformed through complete denitrification accounted for <0-72% of the pore water nitrate reduced. Here, we show that up to 99% of nitrate removal in mangrove sediments is routed through dissimilatory nitrate reduction to ammonium (DNRA).

Denitrification prevails over anammox in tropical mangrove sediments (Goa, India).

Denitrification, anammox (Anx) and di-nitrogen fixation were examined in two mangrove ecosystems- the anthropogenically influenced Divar and the relatively pristine Tuvem. Stratified sampling at 2 cm increments from 0 to 10 cm depth revealed denitrification as the main process of N₂ production in mangrove sediments. At Divar, denitrification was ∼3 times higher than at Tuvem with maximum activity of 224.

Isolation and characterization of Thermanaerothrix daxensis gen. nov., sp. nov., a thermophilic anaerobic bacterium pertaining to the phylum "Chloroflexi", isolated from a deep hot aquifer in the Aquitaine Basin.

A new strictly anaerobic thermophilic multicellular filamentous bacterium (0.2-0.3μm×>100μm), designated GNS-1(T), was isolated from a deep hot aquifer in France.

The chemical-in-μwell: a high-throughput technique for identifying solutes eliciting a chemotactic response in motile bacteria.

Bacteria, and in particular marine bacteria, can be found in environments that are poor in nutrients. To survive, they are able to move toward more favorable niches by a mechanism called chemotaxis, whose first step consists in the detection of substrates by chemoreceptors. We developed a chemotactic assay enabling rapid testing of several hundred different solutes and we identified several molecules eliciting a chemotactic response from two aquatic Shewanella species.

Anaerobic ammonium oxidation mediated by Mn-oxides: from sediment to strain level.

Nitrite and (29)N(2) productions in slurry incubations of anaerobically sediment after (15)NO(3) or (15)NH(4) labelling in the presence of Mn-oxides suggested that anaerobic Mn-oxides mediated nitrification coupled with denitrification in muddy intertidal sediments of Arcachon Bay (SW Atlantic French coast). From this sediment, bacterial strains were isolated and physiologically characterized in terms of Mn-oxides and nitrate reduction as well as potential anaerobic nitrification. One of the isolated strain, identified as Marinobacter daepoensis strain M4AY14, was a denitrifier.

Denitrification: an important pathway for nitrous oxide production in tropical mangrove sediments (Goa, India).

Net nitrous oxide production and denitrification activity were measured in two mangrove ecosystems of Goa, India. The relatively pristine site Tuvem was compared to Divar, which is prone to high nutrient input. Stratified sampling at 2-cm intervals within the 0- to 10-cm depth range showed that N2O production at both the locations decreased with depth.

Caldilinea tarbellica sp. nov., a filamentous, thermophilic, anaerobic bacterium isolated from a deep hot aquifer in the Aquitaine Basin.

An anaerobic, thermophilic, filamentous (0.45 × >100 µm) bacterium, designated D1-25-10-4(T), was isolated from a deep hot aquifer in France. Cells were non-motile and Gram-negative.

Caldinitratiruptor microaerophilus, gen. nov., sp. nov. isolated from a French hot spring (Chaudes-Aigues, Massif Central): a novel cultivated facultative microaerophilic anaerobic thermophile pertaining to the Symbiobacterium branch within the Firmicutes.

A novel facultative microaerophilic nitrate-reducing bacterium designated CA62N(T) was isolated from a thermal spring in France. Cells were non-motile rods (2-3 x 0.2 mum) and showed low cytoplasmic density when observed under a phase-contrast microscope.

Thalassobaculum salexigens sp. nov., a new member of the family Rhodospirillaceae from the NW Mediterranean Sea, and emended description of the genus Thalassobaculum.

A novel Gram-negative bacteria, named CZ41_10a(T), was isolated from coastal surface waters of the north-western Mediterranean Sea. Cells were motile, pleomorphic rods, 1.6 mum long and 0.