Quorum sensing in biofilms: a key mechanism to target in ecotoxicological studies.

Our environment is heavily contaminated by anthropogenic compounds, and this issue constitutes a significant threat to all life forms, including biofilm-forming microorganisms. Cell-cell interactions shape microbial community structures and functions, and pollutants that affect intercellular communications impact biofilm functions and ecological roles. There is a growing interest in environmental science fields for evaluating how anthropogenic pollutants impact cell-cell interactions. In this review, we synthesize existing literature that evaluates the impacts of quorum sensing (QS), which is a widespread density-dependent communication system occurring within many bacterial groups forming biofilms. First, we examine the perturbating effects of environmental contaminants on QS circuits; and our findings reveal that QS is an essential yet underexplored mechanism affected by pollutants. Second, our work highlights that QS is an unsuspected and key resistance mechanism that assists bacteria in dealing with environmental contamination (caused by metals or organic pollutants) and that favors bacterial growth in unfavourable environments. We emphasize the value of considering QS a critical mechanism for monitoring microbial responses in ecotoxicology. Ultimately, we determine that QS circuits constitute promising targets for innovative biotechnological approaches with major perspectives for applications in the field of environmental science.

Features of the Opportunistic Behaviour of the Marine Bacterium Marinobacter algicola in the Microalga Ostreococcus tauri Phycosphere.

Although interactions between microalgae and bacteria are observed in both natural environment and the laboratory, the modalities of coexistence of bacteria inside microalgae phycospheres in laboratory cultures are mostly unknown. Here, we focused on well-controlled cultures of the model green picoalga Ostreococcus tauri and the most abundant member of its phycosphere, Marinobacter algicola. The prevalence of M. algicola in O. tauri cultures raises questions about how this bacterium maintains itself under laboratory conditions in the microalga culture. The results showed that M. algicola did not promote O. tauri growth in the absence of vitamin B12 while M. algicola depended on O. tauri to grow in synthetic medium, most likely to obtain organic carbon sources provided by the microalgae. M. algicola grew on a range of lipids, including triacylglycerols that are known to be produced by O. tauri in culture during abiotic stress. Genomic screening revealed the absence of genes of two particular modes of quorum-sensing in Marinobacter genomes which refutes the idea that these bacterial communication systems operate in this genus. To date, the 'opportunistic' behaviour of M. algicola in the laboratory is limited to several phytoplanktonic species including Chlorophyta such as O. tauri. This would indicate a preferential occurrence of M. algicola in association with these specific microalgae under optimum laboratory conditions.

Description of Palleronia rufa sp. nov., a biofilm-forming and AHL-producing Rhodobacteraceae, reclassification of Hwanghaeicola aestuarii as Palleronia aestuarii comb. nov., Maribius pontilimi as Palleronia pontilimi comb. nov., Maribius salinus as Palleronia salina comb. nov., Maribius pelagius as Palleronia pelagia comb. nov. and emended description of the genus Palleronia.

Strain MOLA 401T was isolated from marine waters in the southwest lagoon of New Caledonia and was shown previously to produce an unusual diversity of quorum sensing signaling molecules. This strain was Gram-negative, formed non-motile cocci and colonies were caramel. Optimum growth conditions were 30°C, pH 8 and 3% NaCl (w/v). Based on 16S rRNA gene sequence analysis, this strain was found to be closely related to Pseudomaribius aestuariivivens NBRC 113039T (96.9% of similarity), Maribius pontilimi DSM 104950T (96.4% of similarity) and Palleronia marisminoris LMG 22959T (96.3% of similarity), belonging to the Roseobacter group within the family Rhodobacteraceae. As its closest relatives, strain MOLA 401T is able to form a biofilm on polystyrene, supporting the view of Roseobacter group strains as prolific surface colonizers. An in-depth genomic study allowed us to affiliate strain MOLA 401T as a new species of genus Palleronia and to reaffiliate some of its closest relatives in this genus. Consequently, we describe strain MOLA 401T (DSM 106827T=CIP 111607T=BBCC 401T) for which we propose the name Palleronia rufa sp. nov. We also propose to emend the description of the genus Palleronia and to reclassify Maribius and Hwanghaeicola species as Palleronia species.

Biofilm formation as a microbial strategy to assimilate particulate substrates.

In most ecosystems, a large part of the organic carbon is not solubilized in the water phase. Rather, it occurs as particles made of aggregated hydrophobic and/or polymeric natural or man-made organic compounds. These particulate substrates are degraded by extracellular digestion/solubilization implemented by heterotrophic bacteria that form biofilms on them. Organic particle-degrading biofilms are widespread and have been observed in aquatic and terrestrial natural ecosystems, in polluted and man-driven environments and in the digestive tracts of animals. They have central ecological functions as they are major players in carbon recycling and pollution removal. The aim of this review is to highlight bacterial adhesion and biofilm formation as central mechanisms to exploit the nutritive potential of organic particles. It focuses on the mechanisms that allow access and assimilation of non-dissolved organic carbon, and considers the advantage provided by biofilms for gaining a net benefit from feeding on particulate substrates. Cooperative and competitive interactions taking place in biofilms feeding on particulate substrates are also discussed.

Pleomorphochaeta naphthae sp. nov., a new anaerobic fermentative bacterium isolated from an oil field.

A novel anaerobic fermentative bacterium, strain SEBR 4209T, was isolated from a water sample of a Congolese oil field. Strain SEBR 4209T is phylogenetically related to the genus Pleomorphochaeta, in the family Spirochaetaceae. Its closest relatives are Pleomorphochaeta caudata SEBR 4223T (94.5 % 16S rRNA gene sequence similarity) and Pleomorphochaeta multiformis MO-SPC2T (94.3 % similarity). Like the other members of this genus, cells have a pleomorphic morphology, in particular an annular shape and long stalks. Optimal growth was observed at 37 °C, at pH between 6.8 and 7.0, and with 40 g l-1 NaCl. This strain was only able to grow by fermentation of carbohydrates. The fermentation products from glucose utilization were acetate, ethanol, CO2 and H2. Predominant fatty acids were C14 : 0, C14 : 0 DMA, C16 : 0 and C16 : 1ω7c. The major polar lipids were phosphoglycolipids, phospholipids and glycolipids. The G+C content of the DNA was 29.6 mol%. Based on phenotypic characteristics and phylogenetic traits, strain SEBR 4209T is considered to represent a novel species of the genus Pleomorphochaeta, for which the name Pleomorphochaetanaphthae sp. nov. is proposed. The type strain is SEBR 4209T (=DSM 104684T=JCM 31871T).

Pleomorphochaeta caudata gen. nov., sp. nov., an anaerobic bacterium isolated from an offshore oil well, reclassification of Sphaerochaeta multiformis MO-SPC2T as Pleomorphochaeta multiformis MO-SPC2T comb. nov. as the type strain of this novel genus and emended description of the genus Sphaerochaeta.

A strictly anaerobic Gram-stain-negative bacterium, designated strain SEBR 4223T, was isolated from the production water of an offshore Congolese oil field. Cells were non-motile, pleomorphic and had spherical, annular or budding shapes, often exhibiting long stalks. Strain SEBR 4223T grew on a range of carbohydrates, optimally at 37 °C and pH 7, in a medium containing 40 g l-1 NaCl. Predominant fatty acids were C14 : 0, C14 : 0 DMA, C16 : 0 and C16 : 1ω7c and the major polar lipids were phosphoglycolipids, phospholipids, glycolipids and diphosphatidylglycerol. The G+C content of the DNA was 28.7 mol%. Phylogenetic analysis, based on the 16S rRNA gene sequence, showed that strain SEBR 4223T and Sphaerochaeta multiformis MO-SPC2T formed a cluster with similarity to other species of the genus Sphaerochaeta of of less than 86 %. On the basis of the phenotypic characteristics and taxonomic analyses, we propose a novel genus, Pleomorphochaeta gen. nov., to accommodate the novel species Pleomorphochaeta caudata sp. nov., with SEBR 4223T (=DSM 103077T=JCM 31 475T) as the type strain. We also propose the reclassification of Sphaerochaeta multiformis MO SPC2T as Pleomorphochaeta multiformis MO-SPC2T comb. nov., the type strain of this novel genus and emend description of the genus Sphaerochaeta.

Pleionea mediterranea gen. nov., sp. nov., a gammaproteobacterium isolated from coastal seawater.

A Gram-negative, aerobic, cream-pigmented, non-motile, non-spore-forming straight rod, strain MOLA115(T), was isolated from a coastal water sample from the Mediterranean Sea. On the basis of phylogenetic analysis of the 16S rRNA gene sequences, strain MOLA115(T) was shown to belong to the Gammaproteobacteria, adjacent to members of the genera Marinicella, Arenicella and Kangiella, sharing less than 89 % 16S rRNA gene sequence similarity with strains of all recognized species within the Gammaproteobacteria. The only isoprenoid quinone was ubiquinone-8. Polar lipids in strain MOLA115(T) included phosphatidylethanolamine, an aminolipid, phosphatidylglycerol and an aminophospholipid. Fatty acid analysis revealed iso-C15 : 0 and iso-C17 : 1ω9c to be the dominant components. The DNA G+C content was 44.5 mol%. Based upon the phenotypic and phylogenetic data, we propose that strain MOLA115(T) should be considered to represent a novel species in a new genus, for which the name Pleionea mediterranea gen. nov., sp. nov. is proposed. The type strain of Pleionea mediterranea is MOLA115(T) ( = CIP 110343(T) = DSM 25350(T)).

Pedobacter tournemirensis sp. nov., isolated from a fault water sample of a deep Toarcian argillite layer.

A Gram-negative bacterium, designated TF5-37.2-LB10(T), was isolated from subsurface water of the Toarcian geological layer of Tournemire, France. Cells were non-motile straight rods that formed cream to light pink colonies on 10-fold diluted LB agar. Strain TF5-37.2-LB10(T) contained menaquinone 7 and its major fatty acids were iso-C(15 : 0), summed feature 3 (iso-C(15 : 0) 2-OH and/or C(16 : 1)ω7c), iso-C(17 : 0) 3-OH and iso-C(17 : 1)ω9c. The G+C content of the genomic DNA was 46 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed strain TF5-37.2-LB10(T) within the genus Pedobacter, family Sphingobacteriaceae. Pedobacter composti TR6-06(T) and Pedobacter oryzae DSM 19973(T) were the closest phylogenetic relatives (93.5 and 93.3 % 16S rRNA gene sequence similarity, respectively). On the basis of 16S rRNA gene sequence comparison and physiological and biochemical characteristics, strain TF5-37.2-LB10(T) represents a novel species of the genus Pedobacter, for which the name Pedobacter tournemirensis sp. nov. is proposed. The type strain is TF5-37.2-LB10(T) (= DSM 23085(T) = CIP 110085(T) = MOLA 820(T)).

Eionea nigra gen. nov., sp. nov., a gammaproteobacterium from the Mediterranean Sea.

A novel aerobic, gram-negative bacterial strain, designated 17X/A02/237(T), was isolated from waters of the coastal north-western Mediterranean Sea. Cells were motile straight rods and formed dark-grey colonies on marine agar medium. Strain 17X/A02/237(T) contained ubiquinone Q-8 and its major fatty acids were C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH, C(18 : 1)ω7c, C(16 : 0), C(18 : 0) and C(10 : 0) 3-OH. The G+C content of the genomic DNA was 47.5 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed the strain in the class Gammaproteobacteria. Based on 16S rRNA gene sequence data, as well as physiological and biochemical characteristics, this isolate represents a novel species of a new genus, for which the name of Eionea nigra gen. nov., sp. nov. is proposed. The type strain is 17X/A02/237(T) ( = DSM 19752(T) = CIP 109759(T) = MOLA 288(T)).

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 0.7 mum wide and formed cream colonies on marine agar medium. The G+C content of the genomic DNA was 65 mol%. Phylogenetic analysis of 16S rRNA gene sequences placed the new isolate in the genus Thalassobaculum, a member of the family Rhodospirillaceae, class Alphaproteobacteria. Unlike Thalassobaculum litoreum CL-GR58(T), its closest relative, strain CZ41_10a(T) was unable to grow anaerobically and did not exhibit nitrate reductase activity. On the basis of DNA-DNA hybridization, fatty acid content and physiological and biochemical characteristics, this isolate represents a novel species for which the name Thalassobaculum salexigens sp. nov. is proposed. The type strain is CZ41_10a(T) (=DSM 19539(T)=CIP 109604(T)=MOLA [corrected] 84(T)). An emended description of the genus Thalassobaculum is also given.

Haliea rubra sp. nov., a member of the Gammaproteobacteria from the Mediterranean Sea.

A novel aerobic, Gram-negative bacterium, designated strain CM41_15a(T), was isolated from the surface of coastal waters of the north-western Mediterranean Sea. Cells were non-motile straight rods that formed red colonies on marine agar medium. The G+C content of the genomic DNA was 65 mol %. Phylogenetic analysis of the 16S rRNA gene sequence placed the strain in the genus Haliea within the class Gammaproteobacteria. On the basis of the 16S rRNA gene sequence comparison and physiological and biochemical characteristics, strain CM41_15a(T) represents a novel species, for which the name Haliea rubra sp. nov. is proposed. The type strain is CM41_15a(T) (=DSM 19751(T)=CIP 109758(T)=MOLA 104(T)).

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

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)).

Nisaea denitrificans gen. nov., sp. nov. and Nisaea nitritireducens sp. nov., two novel members of the class Alphaproteobacteria from the Mediterranean Sea.

Two novel Gram-negative bacteria, designated strains DR41_21(T) and DR41_18(T), were isolated from coastal, surface waters of the north-western Mediterranean Sea. The cells were motile, pleomorphic rods, 2.9 microm long and 0.9 microm wide and formed cream colonies on marine agar medium. The G+C content of the genomic DNA was 60 mol%. Phylogenetic analysis of 16S rRNA gene sequences positioned the isolates in the class Alphaproteobacteria within the family Rhodospirillaceae. The 16S rRNA gene sequence similarity of the two strains was 98.8 % but DNA-DNA hybridization indicated only 55 % relatedness. Strain DR41_21(T) was able to denitrify and possessed nirK and nosZ genes, unlike strain DR41_18(T), which possessed only nirK. These isolates represent two novel species of a new genus, Nisaea gen. nov., for which the names Nisaea denitrificans sp. nov. and Nisaea nitritireducens sp. nov. are proposed. The type strain of Nisaea denitrificans is DR41_21(T) (=DSM 18348(T)=CIP 109265(T)=OOB 129(T)) and the type strain of Nisaea nitritireducens is DR41_18(T) (=DSM 19540(T)=CIP 109601(T)=OOB 128(T)).

Balneola alkaliphila sp. nov., a marine bacterium isolated from the Mediterranean Sea.

A novel aerobic, Gram-negative bacterium, designated strain CM41_14b(T), was isolated from surface waters in the coastal north-western Mediterranean Sea. Cells were non-motile, straight rods, 2.6 microm long and 0.7 microm wide and formed pale-orange colonies on marine agar medium. The G+C content of the genomic DNA was 39 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence placed the strain within the genus Balneola (phylum Bacteroidetes). On the basis of 16S rRNA gene sequence comparisons, and physiological and biochemical characteristics, the isolate represents a novel species for which the name Balneola alkaliphila sp. nov. is proposed. The type strain is CM41_14b(T) (=DSM 19538(T)=CIP 109603(T)=OOB 103(T)).

Haliea salexigens gen. nov., sp. nov., a member of the Gammaproteobacteria from the Mediterranean Sea.

A novel aerobic, Gram-negative bacterium, designated 3X/A02/235T, was isolated from the surface of coastal waters in the north-western Mediterranean Sea. Cells were motile, straight rods, 1.6 microm long and 0.5 microm wide, and formed cream colonies on marine agar medium. The G+C content of the genomic DNA was 61 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed the strain in the class Gammaproteobacteria and within the family Alteromonadaceae. On the basis of 16S rRNA gene sequence comparisons and physiological and biochemical characteristics, this isolate represents a novel species of a novel genus, for which the name Haliea salexigens gen. nov., sp. nov. is proposed. The type strain of Haliea salexigens is 3X/A02/235T (=DSM 19537T =CIP 109602T =MOLA 286T).

Balneola vulgaris gen. nov., sp. nov., a member of the phylum Bacteroidetes from the north-western Mediterranean Sea.

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)).

Continuous enrichment culture and molecular monitoring to investigate the microbial diversity of thermophiles inhabiting deep-sea hydrothermal ecosystems.

The microflora developing during a continuous enrichment culture from a hydrothermal chimney sample was investigated by molecular methods. The culture was performed in a gas-lift bioreactor under anaerobic conditions, at 90 degrees C and pH 6.5, on a complex medium containing sulfur as the terminal electron acceptor. Archaeal and bacterial diversity was studied. Microorganisms affiliated with the genera Pyrococcus, Marinitoga, and Bacillus were detected through DGGE analysis of 16S rDNA. Additional sequences phylogenetically related to Thermococcus and epsilon-Proteobacteria were detected by cloning and sequencing of 16S rDNA from two samples of the enrichment culture. In comparison, the sequences retrieved from cloning analysis from an enrichment culture performed in a flask (batch condition) using the same culture medium showed that only members of the genus Thermococcus were cultivated. Therefore, continuous enrichment culture using the gas-lift bioreactor can be considered as an efficient and improved method for investigating microbial communities originating from deep-sea hydrothermal vents.

Thermosipho atlanticus sp. nov., a novel member of the Thermotogales isolated from a Mid-Atlantic Ridge hydrothermal vent.

A novel anaerobic, thermophilic and heterotrophic bacterium, designated strain DV1140(T), was isolated from a deep-sea hydrothermal vent sample from the Mid-Atlantic Ridge. The cells were non-motile straight rods, 1.8 microm long and 0.4 microm wide, surrounded by an outer sheath-like structure (toga). They grew at 45-80 degrees C (optimum 65 degrees C), pH 5.0-9.0 (optimum pH 6.0) and at sea salt concentrations of 20-60 g l(-1) (optimum 30 g l(-1)). Strain DV1140(T) was able to ferment yeast extract, peptone, brain heart infusion, gelatin, starch, galactose, arabinose, glucose, trehalose and cellobiose. The fermentation products identified on glucose in the presence of yeast extract and peptone were acetate, isovalerate and hydrogen. The G+C content of the genomic DNA was 33 mol%. Phylogenetic analysis of the 16S rRNA gene sequence (GenBank accession number AJ577471) located the strain within the genus Thermosipho in the bacterial domain. On the basis of 16S rRNA gene sequence comparisons, and physiological and biochemical characteristics, the isolate represents a novel species, for which the name Thermosipho atlanticus sp. nov. is proposed. The type strain is DV1140(T) (=CIP 108053(T)=DSM 15807(T)).

Tepidibacter formicigenes sp. nov., a novel spore-forming bacterium isolated from a Mid-Atlantic Ridge hydrothermal vent.

A novel anaerobic, Gram-positive, sporulating and strictly chemoorganoheterotrophic bacterium, designated strain DV1184(T), was isolated from a deep-sea hydrothermal vent sample from the Mid-Atlantic Ridge. The cells were short, straight rods (4 micro m long and 0.8 micro m wide) and were motile with peritrichous flagella. They grew between 35 and 55 degrees C (optimum, 45 degrees C), between pH 5.0 and 8.0 (optimum, 6.0) and at 20-60 g sea salts l(-1) (optimum sea salts concentration, 30 g l(-1)). Strain DV1184(T) was able to ferment yeast extract, tryptone, peptone, glucose, sucrose, maltose and pyruvate. The main fermentation products from glucose were (in decreasing order) formate, acetate and ethanol. The genomic DNA G+C content was 29 mol%. Phylogenetic analysis of the 16S rRNA gene located the strain within cluster XI of the lineage that encompasses the genus Clostridium and related genera in the bacterial domain. On the basis of 16S rDNA sequence comparison and physiological and biochemical characteristics, it is proposed that the isolate should be described as a novel species, Tepidibacter formicigenes sp. nov. The type strain is DV1184(T) (=CIP 107893(T)=DSM 15518(T)).