Methanobacterium alkalithermotolerans sp. nov., a novel alkaliphilic and hydrogen-utilizing methanogen isolated from an alkaline geothermal spring (La Crouen, New Caledonia).

An anaerobic, hydrogenotrophic methane-producing archaeon was isolated from an alkaline thermal spring (42 °C, pH 9.0) in New Caledonia. This methanogen, designated strain CANT, is alkaliphilic, thermotolerant, with Gram-positive staining non-motile cells. Strain CANT grows autotrophically using hydrogen exclusively as an energy source and carbon dioxide as the sole carbon source (without the requirement of yeast extract or other organic compounds). It grows at 20-45 °C (optimum, 45 °C) and pH 7.3-9.7 (optimum, pH 9.0). NaCl is not required for growth (optimum 0 %) but is tolerated up to 1.5 %. It resists novobiocin, streptomycin and vancomycin but is inhibited by ampicillin and penicillin, among other antibiotics. The genome consists of a circular chromosome (2.2 Mb) containing 2126 predicted protein-encoding genes with a G+C content of 36.4 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain CANT is a member of the genus Methanobacterium, most closely related to the alkaliphilic Methanobacterium alcaliphilum WeN4T with 98.5 % 16S rRNA gene sequence identity. The genomes of strain CANT and M. alcaliphilum DSM 3459, sequenced in this study, share 71.6 % average nucleotide identity and 14.0 % digital DNA-DNA hybridization. Therefore, phylogenetic and physiological results indicate that strain CANT represents a novel species, for which the name Methanobacterium alkalithermotolerans sp. nov. is proposed, and strain CANT (=DSM 102889T= JCM 31304T) is assigned as the type strain.

Alkalicella caledoniensis gen. nov., sp. nov., a novel alkaliphilic anaerobic bacterium isolated from 'La Crouen' alkaline thermal spring, New Caledonia.

A novel anaerobic, alkaliphilic, mesophilic, Gram-stain-positive, endospore-forming bacterium was isolated from an alkaline thermal spring (42 °C, pH 9.0) in New Caledonia. This bacterium, designated strain LB2T, grew at 25-50 °C (optimum, 37 °C) and pH 8.2-10.8 (optimum, pH 9.5). Added NaCl was not required for growth (optimum, 0-1 %) but was tolerated up to 7 %. Strain LB2T utilized a limited range of substrates, such as peptone, pyruvate, yeast extract and xylose. End products detected from pyruvate fermentation were acetate and formate. Both ferric citrate and thiosulfate were used as electron acceptors. Elemental sulphur, nitrate, nitrite, fumarate, sulphate, sulfite and DMSO were not used as terminal electron acceptors. The two major cellular fatty acids were iso-C15 : 0 and C16 : 0. The genome consists of a circular chromosome (3.7 Mb) containing 3626 predicted protein-encoding genes with a G+C content of 36.2 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the isolate is a member of the family Proteinivoraceae, order Clostridiales within the phylum Firmicutes. Strain LB2T was most closely related to the thermophilic Anaerobranca gottschalkii LBS3T (93.2 % 16S rRNA gene sequence identity). Genome-based analysis of average nucleotide identity and digital DNA-DNA hybridization of strain LB2T with A. gottschalkii LBS3T showed respective values of 70.8 and 13.4 %. Based on phylogenetic, genomic, chemotaxonomic and physiological properties, strain LB2T is proposed to represent the first species of a novel genus, for which the name Alkalicella caledoniensis gen. nov., sp. nov. is proposed (type strain LB2T=DSM 100588T=JCM 30958T).

Abundance and diversity of prokaryotes in ephemeral hypersaline lake Chott El Jerid using Illumina Miseq sequencing, DGGE and qPCR assays.

Chott El Jerid is the largest hypersaline ephemeral lake in southern Tunisian Sahara desert and is one of the biggest depressions at the North of Africa. This study aimed to investigate the diversity and abundance of microbial communities inhabiting Chott El Jerid during wet season (when it was flooded), using molecular methods [Illumina Miseq sequencing, DGGE and qPCR (qPCR)]. 16S rRNA gene analyses revealed that bacterial community was dominated by Proteobacteria (especially Ralstonia species), followed by Firmicutes, Bacteroidetes, Cyanobacteria, Actinobacteria and Verrucomicrobia. The results obtained using prokaryotic universal primers showed low relative abundance of Archaea dominated by few OTUs related to Methanosarcinaceae and Methanomassiliicoccaceae families and the presence of sulfate-reducing Archaea affiliated with Archaeoglobus. However, the results obtained using Archaea-specific primers showed that archaeal community was mainly composed of aerobic Halobacteria (especially Halorubrum species) and anaerobic members of Methanomicrobia. These results also provided evidence for the presence of members of the genus Halohasta in this environment. qPCR results revealed that Archaea were more abundant in studied samples than Bacteria. The sulfate-reducing Bacteria were also found abundant (~ one-third of the bacterial community) and outnumbered methanogens, suggesting their potential important role in this sulfate-rich and hypersaline ecosystem.

Serpentinicella alkaliphila gen. nov., sp. nov., a novel alkaliphilic anaerobic bacterium isolated from the serpentinite-hosted Prony hydrothermal field, New Caledonia.

A novel anaerobic, alkaliphilic, Gram-stain-positive, spore-forming bacterium was isolated from a carbonaceous hydrothermal chimney in Prony Bay, New Caledonia. This bacterium, designated strain 3bT, grew at temperatures from 30 to 43 °C (optimum 37 °C) and at pH between 7.8 and 10.1 (optimum 9.5). Added NaCl was not required for growth (optimum 0-0.2 %, w/v), but was tolerated at up to 4 %. Yeast extract was required for growth. Strain 3bT utilized crotonate, lactate and pyruvate, but not sugars. Crotonate was dismutated to acetate and butyrate. Lactate was disproportionated to acetate and propionate. Pyruvate was degraded to acetate plus trace amounts of hydrogen. Growth on lactate was improved by the addition of fumarate, which was used as an electron acceptor and converted to succinate. Sulfate, thiosulfate, elemental sulfur, sulfite, nitrate, nitrite, FeCl3, Fe(III)-citrate, Fe(III)-EDTA, chromate, arsenate, selenate and DMSO were not used as terminal electron acceptors. The G+C content of the genomic DNA was 33.2 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the isolate is a member of the family Clostridiaceae, order Clostridiales within the phylum Firmicutes. Strain 3bT was most closely related to 'Alkaliphilus hydrothermalis' FatMR1T (92.2 % 16S rRNA gene sequence similarity), and was positioned approximately equidistantly between the genera Alkaliphilus, Anaerovirgula and Natronincola. On the basis of phylogenetic, genetic, chemotaxonomic and physiological properties, strain 3bT is proposed to represent a novel species of a new genus, for which the name Serpentinicella alkaliphila gen. nov., sp. nov. is proposed. The type strain of Serpentinicella alkaliphila is 3bT (=DSM 100013T=JCM 30645T).

Prokaryotic diversity in a Tunisian hypersaline lake, Chott El Jerid.

Prokaryotic diversity was investigated in a Tunisian salt lake, Chott El Jerid, by quantitative real-time PCR, denaturing gradient gel electrophoresis (DGGE) fingerprinting methods targeting the 16S rRNA gene and culture-dependent methods. Two different samples S1-10 and S2-10 were taken from under the salt crust of Chott El Jerid in the dry season. DGGE analysis revealed that bacterial sequences were related to Firmicutes, Proteobacteria, unclassified bacteria, and Deinococcus-Thermus phyla. Anaerobic fermentative and sulfate-reducing bacteria were also detected in this ecosystem. Within the domain archaea, all sequences were affiliated to Euryarchaeota phylum. Quantitative real-time PCR showed that 16S rRNA gene copy numbers of bacteria was 5 × 10(6) DNA copies g(-1) whereas archaea varied between 5 × 10(5) and 10(6) DNA copies g(-1) in these samples. Eight anaerobic halophilic fermentative bacterial strains were isolated and affiliated with the species Halanaerobium alcaliphilum, Halanaerobium saccharolyticum, and Sporohalobacter salinus. These data showed an abundant and diverse microbial community detected in the hypersaline thalassohaline environment of Chott El Jerid.

Acetoanaerobium pronyense sp. nov., an anaerobic alkaliphilic bacterium isolated from a carbonate chimney of the Prony Hydrothermal Field (New Caledonia).

A novel anaerobic bacterial strain, ST07-YET, was isolated from a carbonate chimney of the Prony Hydrothermal Field (PHF) in New Caledonia. Cells were Gram-stain-positive, straight rods (0.7-0.8 × 3.0-5.0 µm) and motile by means of lateral flagella. Strain ST07-YET was mesophilic (optimum 35 °C), moderately alkaliphilic and halotolerant (optimum pH 8.7 and 5 g l- 1 NaCl). Elemental sulfur, sulfate, thiosulfate, sulfite, nitrate and nitrite were not used as terminal electron acceptors. Yeast extract, peptone, tryptone, Casamino acids, crotonate, pyruvate, galactose, maltose, sucrose, ribose, trehalose and glucose were used as carbon sources. Glucose fermentation led to acetate, H2 and CO2 formation. Arginine, serine, histidine, lysine, methionine and cysteine improved growth, but the Stickland reaction was negative for the combinations of amino acids tested. The major metabolic products from yeast extract fermentation were H2, CO2, acetate, butyrate, isobutyrate, isovalerate and propionate. The predominant cellular fatty acids were C16 : 0, C16 : 1cis9, C14 : 0 and C16 : 1cis7 (>5 % of total fatty acids). The G+C content of the genomic DNA was 32.9 mol%. Phylogenetic analysis revealed that strain ST07-YET was most closely related to Clostridium sticklandii DSM 519T and Acetoanaerobium noterae NOT-3T (96.7 % and 96.8 % 16S rRNA gene sequence similarity, respectively). On the basis of phylogenetic, chemotaxonomic and physiological properties, strain ST07-YET is proposed to represent a novel species of the genus Acetoanaerobium (order Clostridiales, phylum Firmicutes) with the name Acetoanaerobium pronyense sp. nov. The type strain is ST07-YET ( = DSM 27512T = JCM 19400T).

Metabolic challenges and key players in serpentinite-hosted microbial ecosystems.

Serpentinite-hosted systems are amongst the most challenging environments for life on Earth. Serpentinization, a geochemical alteration of exposed ultramafic rock, produces hydrothermal fluids enriched in abiotically derived hydrogen (H2), methane (CH4), and small organic molecules. The hyperalkaline pH of these fluids poses a great challenge for metabolic energy and nutrient acquisition, curbing the cellular membrane potential and limiting electron acceptor, carbon, and phosphorous availability. Nevertheless, serpentinization supports the growth of diverse microbial communities whose metabolic make-up might shed light on the beginning of life on Earth and potentially elsewhere. Here, we outline current hypotheses on metabolic energy production, carbon fixation, and nutrient acquisition in serpentinizing environments. A taxonomic survey is performed for each important metabolic function, highlighting potential key players such as H2 and CH4 cycling Serpentinimonas, Hydrogenophaga, Methanobacteriales, Methanosarcinales, and novel candidate phyla. Methodological biases of the available data and future approaches are discussed.

Microbial taxa related to natural hydrogen and methane emissions in serpentinite-hosted hyperalkaline springs of New Caledonia.

The southeastern part of New Caledonia main island (Grande Terre) is the location of a large ophiolitic formation that hosts several hyperalkaline springs discharging high pH (∼11) and warm (<40°C) fluids enriched in methane (CH4) and hydrogen (H2). These waters are produced by the serpentinization of the ultrabasic rock formations. Molecular surveys had previously revealed the prokaryotic diversity of some of these New Caledonian springs, especially from the submarine chimneys of Prony Bay hydrothermal field. Here we investigate the microbial community of hyperalkaline waters from on-land springs and their relationships with elevated concentrations of dissolved H2 (21.1-721.3 µmol/L) and CH4 (153.0-376.6 µmol/L). 16S rRNA gene analyses (metabarcoding and qPCR) provided evidence of abundant and diverse prokaryotic communities inhabiting hyperalkaline fluids at all the collected springs. The abundance of prokaryotes was positively correlated to the H2/CH4 ratio. Prokaryotes consisted mainly of bacteria that use H2 as an energy source, such as microaerophilic Hydrogenophaga/Serpentinimonas (detected in all sources on land) or anaerobic sulfate-reducing Desulfonatronum, which were exclusively found in the most reducing (Eh ref H2 ∼ -700 mV) and the most H2-enriched waters discharging at the intertidal spring of the Bain des Japonais. The relative abundance of a specific group of uncultured Methanosarcinales that thrive in serpentinization-driven ecosystems emitting H2, considered potential H2-consuming methanogens, was positively correlated with CH4 concentrations, and negatively correlated to the relative abundance of methylotrophic Gammaproteobacteria. Firmicutes were also numerous in hyperalkaline waters, and their relative abundance (e.g., Gracilibacter or Dethiobacter) was proportional to the dissolved H2 concentrations, but their role in the H2 budget remains to be assessed. The prokaryotic communities thriving in New Caledonia hyperalkaline waters are similar to those found in other serpentinite-hosted high-pH waters worldwide, such as Lost City (North Atlantic) and The Cedars (California).

Karenia selliformis bloom dynamics and growth rate estimation in the Sfax harbour (Tunisia), by using automated flow cytometry equipped with image in flow, during autumn 2019.

A Karenia selliformis bloom event in the Gulf of Gabès (Mediterranean Sea), was monitored over 9 days at high frequency during fall 2019, by using an automated flow cytometer (Cytosense, Cytobuoy b.v.) with an image-in-flow attachment. The instrument recorded the shape of the optical signals that lead to the resolution of six cell groups of pico-, nano- and microphytoplankton, during the Harmful Algal Bloom (HAB). K. selliformis cell dimensions derived from the hourly records, enabled to estimate the daily division rate over the bloom period. Results revealed that K. selliformis was the only bloom-forming species and it reached its highest mean abundance the fourth day of the survey. A shift in the nutrient composition occurred with a potential P limitation during the bloom growth and N limitation during the bloom collapse. The co-inertia analysis revealed opposite patterns for K. selliformis and heterotrophic prokaryotes suggesting trophic interactions and possible mixotrophic behaviour of K. selliformis at the end of the bloom. K. selliformis exhibited low growth rates generally < 1 division day-1, which could not explain the observed high abundance. The tide played a crucial role in the dynamics of K. selliformis at a semi-diurnal scale and at spring-neap tide scale and was probably enhancing K. selliformis accumulation.

Contamination of planktonic food webs in the Mediterranean Sea: Setting the frame for the MERITE-HIPPOCAMPE oceanographic cruise (spring 2019).

This paper looks at experiential feedback and the technical and scientific challenges tied to the MERITE-HIPPOCAMPE cruise that took place in the Mediterranean Sea in spring 2019. This cruise proposes an innovative approach to investigate the accumulation and transfer of inorganic and organic contaminants within the planktonic food webs. We present detailed information on how the cruise worked, including 1) the cruise track and sampling stations, 2) the overall strategy, based mainly on the collection of plankton, suspended particles and water at the deep chlorophyll maximum, and the separation of these particles and planktonic organisms into various size fractions, as well as the collection of atmospheric deposition, 3) the operations performed and material used at each station, and 4) the sequence of operations and main parameters analysed. The paper also provides the main environmental conditions that were prevailing during the campaign. Lastly, we present the types of articles produced based on work completed by the cruise that are part of this special issue.

Isotopic compositions of copper and zinc in plankton from the Mediterranean Sea (MERITE-HIPPOCAMPE campaign): Tracing trophic transfer and geogenic inputs.

This study uses Cu and Zn isotopic compositions as proxies of sources and metal transfers in the planktonic food webs from the Mediterranean Sea. Plankton was collected in spring 2019 in the deep chlorophyll maximum (DCM) along a North-South transect including coastal and offshore zones (MERITE-HIPPOCAMPE campaign). δ65Cu and δ66Zn were determined on four planktonic size fractions from 60 to 2000 µm. Combined δ65Cu and δ66Zn with geochemical tracers (Ti, particulate organic phosphorus) showed that geogenic particles were ubiquitous with plankton assemblages. The δ15N ecological tracer showed that planktonic food web was enriched in heavy isotopes of Cu and Zn in the higher trophic levels. δ65Cu were correlated with picoplankton in the offshore zone, and with zooplankton in the southern coastal zone. Firmicutes bacteria were found correlated with δ66Zn in northern and southern coastal zones suggesting decomposition of particulate matter at the DCM. These findings suggest that biogeochemical process may impact Cu and Zn isotopy in the planktonic community.

Proposal that the arsenite-oxidizing organisms Thiomonas cuprina and 'Thiomonas arsenivorans' be reclassified as strains of Thiomonas delicata, and emended description of Thiomonas delicata.

The three As(III)-oxidizing members of the class Betaproteobacteria Thiomonas delicata, Thiomonas cuprina and 'Thiomonas arsenivorans' were isolated from mining sites in geographically distinct areas, namely Japan, Germany and France, respectively. They are all able to oxidize As(III) but only 'T. arsenivorans' and T. cuprina show efficient autotrophic growth with As(III) and are able to grow on a sole carbon source. These two organisms are also motile, whereas T. delicata is not. Only T. cuprina can grow autotrophically on chalcopyrite. The three strains share >99% gene sequence similarity with each other based on their 16S rRNA genes and 16S-23S ITS regions. DNA-DNA hybridization results are above, or close to, the threshold value of 70% recommended for the definition of bacterial species. The three taxa show very similar fatty acid profiles with differences only in five minor fatty acid components. They possess phylogenetic and chemotaxonomic similarities supporting the reclassification of these taxa as a single species. We propose that 'T. arsenivorans' and T. cuprina be reassigned as strains of T. delicata (type strain DSM 17897(T)).

Alkaliphilus serpentinus sp. nov. and Alkaliphilus pronyensis sp. nov., two novel anaerobic alkaliphilic species isolated from the serpentinite-hosted Prony Bay Hydrothermal Field (New Caledonia).

Two novel anaerobic alkaliphilic strains, designated as LacTT and LacVT, were isolated from the Prony Bay Hydrothermal Field (PBHF, New Caledonia). Cells were motile, Gram-positive, terminal endospore-forming rods, displaying a straight to curved morphology during the exponential phase. Strains LacTT and LacVT were mesophilic (optimum 30°C), moderately alkaliphilic (optimum pH 8.2 and 8.7, respectively) and halotolerant (optimum 2% and 2.5% NaCl, respectively). Both strains were able to ferment yeast extract, peptone and casamino acids, but only strain LacTT could use sugars (glucose, maltose and sucrose). Both strains disproportionated crotonate into acetate and butyrate. Phylogenetic analysis revealed that strains LacTT and LacVT shared 96.4% 16S rRNA gene sequence identity and were most closely related to A. peptidifermentans Z-7036, A. namsaraevii X-07-2 and A. hydrothermalis FatMR1 (95.7%-96.3%). Their genome size was of 3.29Mb for strain LacTT and 3.06Mb for strain LacVT with a G+C content of 36.0 and 33.9mol%, respectively. The ANI value between both strains was 73.2 %. Finally, strains LacTT (=DSM 100337=JCM 30643) and LacVT (=DSM 100017=JCM 30644) are proposed as two novel species of the genus Alkaliphilus, order Clostridiales, phylum Firmicutes, Alkaliphilus serpentinus sp. nov. and Alkaliphilus pronyensis sp. nov., respectively. The genomes of the three Alkaliphilus species isolated from PBHF were consistently detected in the PBHF chimney metagenomes, although at very low abundance, but not significantly in the metagenomes of other serpentinizing systems (marine or terrestrial) worldwide, suggesting they represent indigenous members of the PBHF microbial ecosystem.

Procaryotic Diversity and Hydrogenotrophic Methanogenesis in an Alkaline Spring (La Crouen, New Caledonia).

(1) Background: The geothermal spring of La Crouen (New Caledonia) discharges warm (42 °C) alkaline water (pH~9) enriched in dissolved nitrogen with traces of methane, but its microbial diversity has not yet been studied. (2) Methods: Cultivation-dependent and -independent methods (e.g., Illumina sequencing and quantitative PCR based on 16S rRNA gene) were used to describe the prokaryotic diversity of this spring. (3) Results: Prokaryotes were mainly represented by Proteobacteria (57% on average), followed by Cyanobacteria, Chlorofexi, and Candidatus Gracilibacteria (GN02/BD1-5) (each > 5%). Both potential aerobes and anaerobes, as well as mesophilic and thermophilic microorganisms, were identified. Some of them had previously been detected in continental hyperalkaline springs found in serpentinizing environments (The Cedars, Samail, Voltri, and Zambales ophiolites). Gammaproteobacteria, Ca. Gracilibacteria and Thermotogae were significantly more abundant in spring water than in sediments. Potential chemolithotrophs mainly included beta- and gammaproteobacterial genera of sulfate-reducers (Ca. Desulfobacillus), methylotrophs (Methyloversatilis), sulfur-oxidizers (Thiofaba, Thiovirga), or hydrogen-oxidizers (Hydrogenophaga). Methanogens (Methanobacteriales and Methanosarcinales) were the dominant Archaea, as found in serpentinization-driven and deep subsurface ecosystems. A novel alkaliphilic hydrogenotrophic methanogen (strain CAN) belonging to the genus Methanobacterium was isolated, suggesting that hydrogenotrophic methanogenesis occurs at La Crouen.

Efficiency of benthic diatom-associated bacteria in the removal of benzo(a)pyrene and fluoranthene.

We investigated the efficiency of a benthic diatom-associated bacteria in removing benzo(a)pyrene (BaP) and fluoranthene (Flt). The diatom, isolated from a PAH-contaminated sediment of the Bizerte Lagoon (Tunisia), was exposed in axenic and non-axenic cultures to PAHs over 7 days. The diversity of the associated bacteria, both attached (AB) and free-living bacteria (FB), was analyzed by the 16S rRNA amplicon sequencing. The diatom, which maintained continuous growth under PAH treatments, was able to accumulate BaP and Flt, with different efficiencies between axenic and non-axenic cultures. Biodegradation, which constituted the main process for PAH elimination, was enhanced in the presence of bacteria, indicating the co-metabolic synergy of microalgae and associated bacteria in removing BaP and Flt. Diatom and bacteria showed different capacities in the degradation of BaP and Flt. Nitzschia sp. harbored bacterial communities with a distinct composition between attached and free-living bacteria. The AB fraction exhibited higher diversity and abundance relative to FB, while the FB fraction contained genera with the known ability of PAH degradation, such as Marivita, Erythrobacter, and Alcaligenes. Moreover, strains of Staphylococcus and Micrococcus, isolated from the FB community, showed the capacity to grow in the presence of crude oil. These results suggest that a "benthic Nitzschia sp.-associated hydrocarbon-degrading bacteria" consortium can be applied in the bioremediation of PAH-contaminated sites.

Population structure and abundance of arsenite-oxidizing bacteria along an arsenic pollution gradient in waters of the upper isle River Basin, France.

Denaturing gradient gel electrophoresis (DGGE) and quantitative real-time PCR (qPCR) were successfully developed to monitor functional aoxB genes as markers of aerobic arsenite oxidizers. DGGE profiles showed a shift in the structure of the aoxB-carrying bacterial population, composed of members of the Alpha-, Beta- and Gammaproteobacteria, depending on arsenic (As) and E(h) levels in Upper Isle River Basin waters. The highest aoxB gene densities were found in the most As-polluted oxic surface waters but without any significant correlation with environmental factors. Arsenite oxidizers seem to play a key role in As mobility in As-impacted waters.

Prokaryotic Diversity and Distribution Along Physical and Nutrient Gradients in the Tunisian Coastal Waters (South Mediterranean Sea).

Prokaryotes play an important role in biogeochemical cycling in marine ecosystems, but little is known about their diversity and composition, and how they may contribute to the ecological functioning of coastal areas in the South Mediterranean Sea. This study investigated bacterial and archaeal community diversity in seawater samples along the Tunisian coast subject to important physicochemical disturbances. The 16S amplicon sequencing survey revealed higher prokaryotic diversity in the northern Tunisian bays than in southeastern waters (Gulf of Gabès). The major taxonomic groups identified in all samples were Alphaproteobacteria (40.9%), Gammaproteobacteria (18.7%), Marine Group II Euryarchaeota (11.3%), and Cyanobacteria (10.9%). Among them, the relative abundance of Alteromonadales, Prochlorococcus, and some clades of Pelagibacterales (SAR11) significantly differed between the northern and the southern bays, whereas no difference was observed across coastal waters in the archaeal Candidatus Poseidoniales (MGII), Synechococcus, and Pelagibacteraceae (SAR11 clade Ia), for which no relationship was observed with the environmental variables. Both Pseudoalteromonas and Alteromonas levels increased with the increasing salinity, density and nutrients (NH4 + and/or PO4 3-) gradients detected toward the southern waters, while the SAR11 clades Ib and IV and Prochlorococcus, decreased in the shallow, salty and nutrient-rich coastal waters of the Gulf of Gabès. Rhodobacteraceae was positively correlated with Synechococcus and chlorophyll levels, suggesting a relationship with phytoplankton biomass. The present study provides the first insights into planktonic prokaryotic community composition in the South Mediterranean Sea through the analysis of Tunisian seawaters, which may support further investigations on the role of bacterioplankton in the biogeochemistry of these ecosystems.

Impact of sterilization methods on dissolved trace metals concentrations in complex natural samples: Optimization of UV irradiation.

Sterilization is essential for discriminating biotic responses from abiotic reactions in laboratory experiments investigating biogeochemical processes of complex natural samples. However, the conventional methods used to effectively sterilize materials or culture media do not allow sterilizing complex natural samples while maintaining biogeochemical balances. The aim of this study was to develop a low-cost and easy-to-use method to obtain geochemically unmodified and sterilized samples from complex lacustrine or coastal marine ecosystems. In preliminary assays, the impact of several sterilization methods (autoclaving, chemical poisoning, microwave, UV irradiation) on the trace metals balances was studied using borosilicate glass (BG), fluorinated ethylene-propylene (FEP) or polyethylene terephthalate (PET) bottles. Unlike other methods, UV sterilization had minor effects on the distribution of dissolved trace metals. Additional tests using complex lacustrine and coastal marine samples under 10 g/L sediments were performed using a homemade UV sterilization chamber designed to simultaneously irradiate a large number samples. Results showed: •very reproducible UV tests in BG and FEP bottles•faster sterilization using FEP bottles than using BG bottles•low variations of dissolved trace metals concentrations, except for Al, Cu, Fe and Zn.

Hydrostatic Pressure Helps to Cultivate an Original Anaerobic Bacterium From the Atlantis Massif Subseafloor (IODP Expedition 357): Petrocella atlantisensis gen. nov. sp. nov.

Rock-hosted subseafloor habitats are very challenging for life, and current knowledge about microorganisms inhabiting such lithic environments is still limited. This study explored the cultivable microbial diversity in anaerobic enrichment cultures from cores recovered during the International Ocean Discovery Program (IODP) Expedition 357 from the Atlantis Massif (Mid-Atlantic Ridge, 30°N). 16S rRNA gene survey of enrichment cultures grown at 10-25°C and pH 8.5 showed that Firmicutes and Proteobacteria were generally dominant. However, cultivable microbial diversity significantly differed depending on incubation at atmospheric pressure (0.1 MPa), or hydrostatic pressures (HP) mimicking the in situ pressure conditions (8.2 or 14.0 MPa). An original, strictly anaerobic bacterium designated 70B-AT was isolated from core M0070C-3R1 (1150 meter below sea level; 3.5 m below seafloor) only from cultures performed at 14.0 MPa. This strain named Petrocella atlantisensis is a novel species of a new genus within the newly described family Vallitaleaceae (order Clostridiales, phylum Firmicutes). It is a mesophilic, moderately halotolerant and piezophilic chemoorganotroph, able to grow by fermentation of carbohydrates and proteinaceous compounds. Its 3.5 Mb genome contains numerous genes for ABC transporters of sugars and amino acids, and pathways for fermentation of mono- and di-saccharides and amino acids were identified. Genes encoding multimeric [FeFe] hydrogenases and a Rnf complex form the basis to explain hydrogen and energy production in strain 70B-AT. This study outlines the importance of using hydrostatic pressure in culture experiments for isolation and characterization of autochthonous piezophilic microorganisms from subseafloor rocks.

Diversity surveys and evolutionary relationships of aoxB genes in aerobic arsenite-oxidizing bacteria.

A new primer set was designed to specifically amplify ca. 1,100 bp of aoxB genes encoding the As(III) oxidase catalytic subunit from taxonomically diverse aerobic As(III)-oxidizing bacteria. Comparative analysis of AoxB protein sequences showed variable conservation levels and highlighted the conservation of essential amino acids and structural motifs. AoxB phylogeny of pure strains showed well-discriminated taxonomic groups and was similar to 16S rRNA phylogeny. Alphaproteobacteria-, Betaproteobacteria-, and Gammaproteobacteria-related sequences were retrieved from environmental surveys, demonstrating their prevalence in mesophilic As-contaminated soils. Our study underlines the usefulness of the aoxB gene as a functional marker of aerobic As(III) oxidizers.