Woodsholea maritima gen. nov., sp. nov., a marine bacterium with a low diversity of polar lipids

Removal of natural organic matter by ion exchange: Comparing regenerated and non-regenerated columns

Dissolved organic matter (DOM) in water has adverse impacts on the water treatment process and is effectively removed by ion exchange (IEX). Some researchers have proposed the term biological ion exchange (BIEX) for the process of continuous DOM removal by ion exchange without the need for chemical regeneration that results in brine waste. Surface water with moderate dissolved organic carbon (DOC) concentrations (4-6 mg/L) and high sulfate concentrations (80 - 120 mg/L) was fed to two regenerated and two non-regenerated columns for 12,500 bed volumes (9 months) with the goal of investigating the effects of chemical and possibly biological regeneration on long-term IEX operation. Chemically regenerated columns achieved between 60 and 80% DOC removal for the entirety of the experiment, while non-regenerated columns achieved steady DOC removal of ~50%. Inorganic ion analysis showed that biological activity had minimal impact on DOC removal, and the main mechanism of removal was secondary IEX between sulfate (SO₄^2-) and fractions of DOC with high affinities for ion exchange. Fluorescence and specific UV absorbance at 254 nm (SUVA 254) data showed that fractions of DOC with higher SUVA 254 values (terrestrial-like fractions) were better removed by secondary IEX than those with lower SUVA 254 values (aquatic/microbial-like fractions). Scanning electron microscopy showed that biofilms on non-regenerated resins covered 5-15% of the resin surface and are composed of numerous species of bacteria with varying functions, with some protozoa present.

Alkalicaulis satelles gen. nov., sp. nov., a novel haloalkaliphile isolated from a laboratory culture cyanobacterium Geitlerinema species and proposals of Maricaulaceae fam. nov., Robiginitomaculaceae fam. nov., Maricaulales ord. nov. and Hyphomonadales ord. nov

A prosthecate bacterial strain, designated G-192^T, was isolated from decaying biomass of a haloalkaliphilic cyanobacterium Geitlerinema sp. Z-T0701. The cells were aerobic, Gram-negative, non-endospore-forming and dimorphic, occurring either as sessile bacteria with a characteristic stalk or as motile flagellated cells. The strain utilized a limited range of substrates, mostly peptonaceous, but was able to degrade whole proteins. Growth occurred at 5-46 °C (optimum, 35-40 °C), pH 7.3-10.3 (optimum, pH 8.0-9.0), 0-14 % NaCl (v/w; optimum, 2.0-6.0 %, v/w). The G+C content of the genomic DNA of strain G-192^T was 66.8%. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain G-192^T formed a distinct evolutionary lineage within the family Hyphomonadaceae. Strain G-192^T showed the highest 16S rRNA sequence similarity to Glycocaulis profundi ZYF765^T (95.2%), Oceanicaulis stylophorae GISW-4^T (94.2%) and Marinicauda salina WD6-1^T (95.5%). The major cellular fatty acids (>5% of the total) were C_18:1 ω9c, C_18:0 and 11-methyl-C_18:1 ω7c. The major polar lipids were glycolipids and phospholipids. The only respiratory quinone was ubiquinone-10 (Q-10). Based on polyphasic results including phylogenomic data, the novel strain could be distinguished from other genera, which suggests that strain G-192^T represents a novel species of a new genus, for which the name Alkalicaulis satelles gen. nov., sp. nov. is proposed. The type strain is G-192^T (=VKM B-3306^T=KCTC 72746^T). The strain is the first representative of the stalked bacteria associated with a haloalkaliphilic cyanobacterium. Based on phylogenomic indices and phenotypic data, it is proposed to evolve two novel families Maricaulaceae fam. nov. and Robiginitomaculaceae fam. nov. out of the current family Hyphomonadaceae. In addition, it is proposed to place the first two families in the novel order Maricaulales ord. nov. and novel order Hyphomonadales ord. nov. is proposed to accommodate the family Hyphomonadaceae.

Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria

The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.

Vitreimonas flagellata gen. nov., sp. nov., a novel member of the family Hyphomonadaceae isolated from an activated sludge sample

A coccobacilli-shaped proteobacterium, designated strain SYSU XM001T, was isolated from an activated sludge sample collected from JiMei sewage treatment plant, Xiamen, PR China. Cells were Gram-stain-negative, catalase-positive and oxidase-negative. The 16S rRNA gene sequence of strain SYSU XM001T shared less than 92 % sequence identities with members of the class Alphaproteobacteria , with highest sequence similarity to Aquidulcibacter paucihalophilus TH1-2T (91.6 %; family Hyphomonadaceae , order Rhodobacterales ). The strain exhibited growth at 25–37 °C, pH 7.0–9.0 and in the presence of up to 1 % (w/v) NaCl. Its chemotaxonomic features included ubiquinone-10 as the respiratory isoprenologue, iso-C16 : 0, 10-methyl C16 : 0 TSBA and anteiso-C17 : 0 as major cellular fatty acids and monoglycosyldiglyceride, glucuronopyranosyldiglyceride and two unidentified glycolipids as the main polar lipids. The DNA G+C content was determined to be 62.9 % (draft genome). Analyses of the phylogenetic data and differences in the chemotaxonomic and biochemical features from related genera in the family Hyphomonadaceae indicated that strain SYSU XM001T merits representation of a novel species of a novel genus, for which the name Vitreimonas flagellata gen. nov., sp. nov. is proposed. The type strain of Vitreimonas flagellata is SYSU XM001T (=CGMCC 1.16661T=KCTC 62915T).

Bioprospecting potential of microbial communities in solid waste landfills for novel enzymes through metagenomic approach

Landfills are repository for complex microbial diversity responsible for bio-degradation of solid waste. To elucidate this complexity, samples from three different landfill sites of North India (sample V: Bhalswa near Karnal byepass road, New Delhi, India; sample T: Chandigarh, India and sample S3: Una, H.P., India) were analyzed using metagenomic approach. Selected landfill sites had different geographical location, varied in waste composition, size of landfill and climate zone. For comparison, one sample from high altitude (sample J) having less human interference was taken in this study. The aim of this study was to explore microbial diversity of communities responsible for degradation of landfill. Samples were characterized by 16S rRNA gene sequencing. Data from three landfill sites showed abundance of phylum Proteobacteria while less contaminated sample from high altitude showed abundance of phylum Cholroflexi followed by phylum Proteobacteria. The most abundant genus was unknown suggesting that these landfills could be repository for various novel bacterial communities. Sample T was relatively more active in terms of microbial activity. It was relatively abundant in enzymes responsible for dioxin degradation, styrene degradation, steroid degradation, streptomycin biosynthesis, carbapenem biosynthesis, monobactam biosynthesis, furfural degradation pathways while sample J was predicted to be enriched in plant cell wall degrading enzymes. Co-occurrence analysis revealed presence of complex interaction networks between microbial assemblages responsible for bio-degradation of hydrocarbons. The data provides insights about synergetic interactions and functional interplay between bacterial communities in different landfill sites which could be further exploited to develop an effective bioremediation process.

Pre-coagulation coupled with sponge-membrane filtration for organic matter removal and membrane fouling control during drinking water treatment

A new hybrid system was developed in this study for the treatment of drinking water consisting of pre-coagulation using polyaluminium chloride (PACl) and membrane filtration (MF) with sponge cubes acting as biomass carriers (P-SMF). When compared to a conventional MF (CMF) and a MF after coagulation by utilizing PACl (P-MF), better removal of nutrients, UV₂₅₄ and dissolved organic carbon (DOC) (>65%) was obtained from the P-SMF. The accumulation of biopolymers (including polysaccharides and proteins), humic substances, hydrophilic organics, and other small molecular weight (MW) organic matter in the CMF led to the most severe membrane fouling coupled with the highest pore blocking and cake resistance. Pre-coagulation was ineffective in eliminating small MW and hydrophilic organic matter. Conversely, the larger MW organics (i.e. biopolymers and humic substances), small MW organics and hydrophilic organic compounds could be removed in significantly larger quantities in the P-SMF by PACl coagulation. This was achieved via adsorption and the biodegradation by attached biomass on these sponges and by the suspended sludge. Further analyses of the microbial community indicated that the combined addition of PACl and sponges generated a high enrichment of Zoolgloea, Amaricoccus and Reyranella leading to the reduction of biopolymers, and Flexibacter and Sphingobium were linked to the degradation of humic substances. Moreover, some members of Alphaproteobacteria in the P-SMF may be responsible for the removal of low MW organics. These results suggest that the pre-coagulation process coupled with adding sponge in the MF system is a promising technology for mitigating membrane fouling.

Correlation of microbial community structure with pollutants removal, sludge reduction and sludge characteristics in micro-aerobic side-stream reactor coupled membrane bioreactors under different hydraulic retention times

A micro-aerobic side-stream reactor (MSSR) was inserted in returned sludge line of a membrane bioreactor (MBR) for sludge reduction. Three MSSR coupled MBRs (M-MBRs) and an anoxic/oxic MBR (AO-MBR) were operated in parallel to investigate effects of micro-aerobic condition and hydraulic retention time (HRT) of MSSR (HRT_M) on process performance. M-MBRs and AO-MBR were equally effective in COD and NH₄-N removal. Rising HRT_M from 3.3 to 6.7 h increased sludge reduction from 10.8% to 47.5%, and promoted dissolved organic matters release and utilization by enriching hydrolytic, fermentative and predatory bacteria. M-MBR at HRT_M of 3.3 h obtained the highest nitrogen removal, and enriched denitrifiers (Thauera and Hyphomicrobium) in the MSSR. The highest relative abundance of polyphosphate-accumulating organisms was observed in M-MBR at HRT_M of 5.0 h, which achieved the highest phosphorus removal. Prolonging HRT_M to 6.7 h improved sludge dewaterability by enriching floc-formation bacteria (Nannocystis) and inhibiting filamentous bacteria (Candidatus_Alysiosphaera).

Advanced treatment of petrochemical wastewater by combined ozonation and biological aerated filter

The secondary effluent from a petrochemical wastewater treatment plant was treated by biological aerated filter (BAF) before and after ozonation, namely BAF1 and BAF2, respectively. The results showed that BAF2 fed with the ozonized secondary effluent exhibited a high efficiency in degrading organic pollutants. The removal efficiency of COD and NH₄-N was 6.0 ± 3.2 and 48.2~18.6% for BAF1 and 12.5 ± 5.8 and 62.1~40.9% for BAF2, respectively, during the whole operation. The integration system of ozonation and BAF could tolerate a higher organic loading rate. When HRT decreased from 4 to 1 h, COD removal efficiency decreased from 12 to 4% for the BAF1 system, but it kept almost unchanged at high levels of 27-32% for the ozonation-BAF2 system, with around 20% removal by ozonation. The biomass in BAF2 exhibited a higher activity of protease, DHA, and SOUR than that in BAF1. The organic pollutants in influent and effluent of BAF were mainly ester compounds, which were difficult to biodegrade by BAF. The predominant genera in BAF1 were Gemmatimonadaceae uncultured, Thauera, and Thiobacillus, while the dominant genera in BAF2 were Nitrospira, Gemmatimonadaceae uncultured, and Flexibacter, respectively. Overall, BAF2 performed better than BAF1 in organic pollutant removal and microbial activity. The ozonation process was vital for BAF to treat petrochemical secondary effluent.

Cohesive Properties of the Caulobacter crescentus Holdfast Adhesin Are Regulated by a Novel c-di-GMP Effector Protein

When encountering surfaces, many bacteria produce adhesins to facilitate their initial attachment and to irreversibly glue themselves to the solid substrate. A central molecule regulating the processes of this motile-sessile transition is the second messenger c-di-GMP, which stimulates the production of a variety of exopolysaccharide adhesins in different bacterial model organisms. In Caulobacter crescentus, c-di-GMP regulates the synthesis of the polar holdfast adhesin during the cell cycle, yet the molecular and cellular details of this control are currently unknown. Here we identify HfsK, a member of a versatile N-acetyltransferase family, as a novel c-di-GMP effector involved in holdfast biogenesis. Cells lacking HfsK form highly malleable holdfast structures with reduced adhesive strength that cannot support surface colonization. We present indirect evidence that HfsK modifies the polysaccharide component of holdfast to buttress its cohesive properties. HfsK is a soluble protein but associates with the cell membrane during most of the cell cycle. Coincident with peak c-di-GMP levels during the C. crescentus cell cycle, HfsK relocalizes to the cytosol in a c-di-GMP-dependent manner. Our results indicate that this c-di-GMP-mediated dynamic positioning controls HfsK activity, leading to its inactivation at high c-di-GMP levels. A short C-terminal extension is essential for the membrane association, c-di-GMP binding, and activity of HfsK. We propose a model in which c-di-GMP binding leads to the dispersal and inactivation of HfsK as part of holdfast biogenesis progression.

Exopolysaccharide (EPS) adhesins are important determinants of bacterial surface colonization and biofilm formation. Biofilms are a major cause of chronic infections and are responsible for biofouling on water-exposed surfaces. To tackle these problems, it is essential to dissect the processes leading to surface colonization at the molecular and cellular levels. Here we describe a novel c-di-GMP effector, HfsK, that contributes to the cohesive properties and stability of the holdfast adhesin in C. crescentus. We demonstrate for the first time that c-di-GMP, in addition to its role in the regulation of the rate of EPS production, also modulates the physicochemical properties of bacterial adhesins. By demonstrating how c-di-GMP coordinates the activity and subcellular localization of HfsK, we provide a novel understanding of the cellular processes involved in adhesin biogenesis control. Homologs of HfsK are found in representatives of different bacterial phyla, suggesting that they play important roles in various EPS synthesis systems.

Phospholipids and glycolipids mediate proton containment and circulation along the surface of energy-transducing membranes

Proton bioenergetics provides the energy for growth and survival of most organisms in the biosphere ranging from unicellular marine phytoplankton to humans. Chloroplasts harvest light and generate a proton electrochemical gradient (proton motive force) that drives the production of ATP needed for carbon dioxide fixation and plant growth. Mitochondria, bacteria and archaea generate proton motive force to energize growth and other physiologies. Energy transducing membranes are at the heart of proton bioenergetics and are responsible for catalyzing the conversion of energy held in high-energy electrons→electron transport chain→proton motive force→ATP. Whereas the electron transport chain is understood in great detail there are major gaps in understanding mechanisms of proton transfer or circulation during proton bioenergetics. This paper is built on the proposition that phospho- and glyco-glycerolipids form proton transport circuitry at the membrane's surface. By this proposition, an emergent membrane property, termed the hyducton, confines active/unbound protons or hydronium ions to a region of low volume close to the membrane surface. In turn, a von Grotthuß mechanism rapidly moves proton substrate in accordance with nano-electrochemical poles on the membrane surface created by powerful proton pumps such as ATP synthase.

A novel alphaproteobacterial ectosymbiont promotes the growth of the hydrocarbon-rich green alga Botryococcus braunii

Botryococcus braunii is a colony-forming green alga that accumulates large amounts of liquid hydrocarbons within the colony. The utilization of B. braunii for biofuel production is however hindered by its low biomass productivity. Here we describe a novel bacterial ectosymbiont (BOTRYCO-2) that confers higher biomass productivity to B. braunii. 16S rDNA analysis indicated that the sequence of BOTRYCO-2 shows low similarity (<90%) to cultured bacterial species and located BOTRYCO-2 within a phylogenetic lineage consisting of uncultured alphaproteobacterial clones. Fluorescence in situ hybridization (FISH) studies and transmission electric microscopy indicated that BOTRYCO-2 is closely associated with B. braunii colonies. Interestingly, FISH analysis of a water bloom sample also found BOTRYCO-2 bacteria in close association with cyanobacterium Microcystis aeruginosa colonies, suggesting that BOTRYCO-2 relatives have high affinity to phytoplankton colonies. A PCR survey of algal bloom samples revealed that the BOTRYCO-2 lineage is commonly found in Microcystis associated blooms. Growth experiments indicated that B. braunii Ba10 can grow faster and has a higher biomass (1.8-fold) and hydrocarbon (1.5-fold) yield in the presence of BOTRYCO-2. Additionally, BOTRYCO-2 conferred a higher biomass yield to BOT-22, one of the fastest growing strains of B. braunii. We propose the species name 'Candidatus Phycosocius bacilliformis' for BOTRYCO-2.

Bacterial community structure of autotrophic denitrification biocathode by 454 pyrosequencing of the 16S rRNA gene

Few studies have been conducted to explore the community composition in denitrifying biocathode. Herein, the microbial communities of denitrifying biocathodes yielding current of 1 mA (reactor C1) and 1.5 mA (reactor C2) were characterized by 454 pyrosequencing. The nitrate removal efficiencies in C1 and C2 were about 93 and 85%, respectively. The optimization of data generated high-quality sequences of 18509 in C1 and 14857 in C2. Proteobacteria was the predominant phylum, and Bacteroidetes, Chloroflexi, and Planctomycetes were the subdominant groups. Classes of Alphaproteobacteria, Anaerolineae, and Phycisphaerae may benefit the performance of current production and nitrate removal. Twenty-nine dominant operational taxonomic units (OTUs) accounted for 64 and 65% of sequences in C1 and C2, respectively. A denitrifying pathway was constructed based on the phylogenetic analysis and function inferring of the dominant OTUs. Obviously, the 454 pyrosequencing provided a high-resolution profile of bacteria community in denitrifying biocathode.

Accumulation of novel glycolipids and ornithine lipids in Mesorhizobium loti under phosphate deprivation

Glycolipids are found mainly in photosynthetic organisms (plants, algae, and cyanobacteria), Gram-positive bacteria, and a few other bacterial phyla. They serve as membrane lipids and play a role under phosphate deprivation as surrogates for phospholipids. Mesorhizobium loti accumulates different di- and triglycosyl diacylglycerols, synthesized by the processive glycosyltransferase Pgt-Ml, and two so far unknown glycolipids, which were identified in this study by mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy as O-methyl-digalactosyl diacylglycerol (Me-DGD) and glucuronosyl diacylglycerol (GlcAD). Me-DGD is a novel glycolipid, whose synthesis depends on Pgt-Ml activity and the involvement of an unknown methyltransferase, while GlcAD is formed by a novel glycosyltransferase encoded by the open reading frame (ORF) mlr2668, using UDP-glucuronic acid as a sugar donor. Deletion mutants lacking GlcAD are not impaired in growth. Our data suggest that the different glycolipids in Mesorhizobium can mutually replace each other. This may be an adaptation mechanism to enhance the competitiveness in natural environments. A further nonphospholipid in Mesorhizobium was identified as a hydroxylated form of an ornithine lipid with the additional hydroxy group linked to the amide-bound fatty acid, introduced by the hydroxylase OlsD. The presence of this lipid has not been reported for rhizobia yet. The hydroxy group is placed on the C-2 position of the acyl chain as determined by NMR spectroscopy. Furthermore, the isolated ornithine lipids contained up to 80 to 90% d-configured ornithine, a stereoform so far undescribed in bacteria.

Glycocaulis albus sp. nov., a moderately halophilic dimorphic prosthecate bacterium isolated from petroleum-contaminated saline soil

Two novel bacterial strains, SLG210-30A1T and SLG210-19A2, which shared 99.9 % 16S rRNA gene sequence similarity with each other, were isolated from petroleum-contaminated saline soil in Shengli Oilfield, eastern China. Cells were Gram-stain-negative, motile, aerobic, mesophilic and moderately halophilic. They could grow chemoheterotrophically with oxygen as an electron acceptor. Morphologically, cells were typical Caulobacteria-type dimorphic prosthecate bacteria. The genomic DNA G+C contents of strains SLG210-30A1T and SLG210-19A2 were 61.8 mol% and 61.6 mol% respectively. Strain SLG210-30A1T had Q10 as the predominant respiratory ubiquinone, and C16 : 0 (28.4 %), C17 : 0 (11.6 %), C18 : 0 (22.1 %) and C18 : 1ω7c (14.0 %) as the major cellular fatty acids. The polar lipids of the two isolates were some glycolipids, a lipid, a phospholipid, an aminoglycolipid and an aminophospholipid (all unidentified). The 16S rRNA gene sequences of strains SLG210-30A1T and SLG210-19A2 showed the highest similarities with Glycocaulis abyssi MCS 33T (99.8–99.9 %), but low sequence similarities (<94.7 %) with type strains of other members of the family Hyphomonadaceae . However, the DNA–DNA relatedness of G. abyssi MCS 33T to strains SLG210-30A1T and SLG210-19A2 was 37.4±4.4 % and 36.1±1.1 %, respectively. Based on different physiological, biochemical, and phylogenetic characteristics, strains SLG210-30A1T and SLG210-19A2 represent a novel species of the genus Glycocaulis . The name Glycocaulis albus is therefore proposed with strain SLG210-30A1T ( = LMG 27741T = CGMCC 1.12766T) as the type strain. An emended description of the genus Glycocaulis is also provided.

A bifunctional glycosyltransferase from Agrobacterium tumefaciens synthesizes monoglucosyl and glucuronosyl diacylglycerol under phosphate deprivation

Glycolipids are mainly found in phototrophic organisms (like plants and cyanobacteria), in Gram-positive bacteria, and a few other bacterial phyla. Besides the function as bulk membrane lipids, they often play a role under phosphate deprivation as surrogates for phospholipids. The Gram-negative Agrobacterium tumefaciens accumulates four different glycolipids under phosphate deficiency, including digalactosyl diacylglycerol and glucosylgalactosyl diacylglycerol synthesized by a processive glycosyltransferase. The other two glycolipids have now been identified by mass spectrometry and nuclear magnetic resonance spectroscopy as monoglucosyl diacylglycerol and glucuronosyl diacylglycerol. These two lipids are synthesized by a single promiscuous glycosyltransferase encoded by the ORF atu2297, with UDP-glucose or UDP-glucuronic acid as sugar donors. The transfer of sugars differing in their chemistry is a novel feature not observed before for lipid glycosyltransferases. Furthermore, this enzyme is the first glucuronosyl diacylglycerol synthase isolated. Deletion mutants of Agrobacterium lacking monoglucosyl diacylglycerol and glucuronosyl diacylglycerol or all glycolipids are not impaired in growth or virulence during infection of tobacco leaf discs. Our data suggest that the four glycolipids and the nonphospholipid diacylglyceryl trimethylhomoserine can mutually replace each other during phosphate deprivation. This redundancy of different nonphospholipids may represent an adaptation mechanism to enhance the competitiveness in nature.

Draft Genome Sequence of Euryhalocaulis caribicus Strain JL2009T, a New Member of the Family Hyphomonadaceae Isolated from the Caribbean Sea

Euryhalocaulis caribicus strain JL2009(T) is a novel genus and species of the family Hyphomonadaceae and was first isolated from surface water in the Caribbean Sea. Here, we report the first draft genome from this genus. Its genome contains genes encoding proteins that are involved in organic acid metabolism and probable low-affinity inorganic phosphate transporters, which suggests its competence in oligotrophic oceans.

Cauliform bacteria lacking phospholipids from an abyssal hydrothermal vent: proposal of Glycocaulis abyssi gen. nov., sp. nov., belonging to the family Hyphomonadaceae

Cauliform bacteria are prosthecate bacteria often specialized for oligotrophic environments. A polyphasic approach, comprising 16S rRNA gene sequencing, lipid analysis and salt tolerance characterizations, was used to clarify the taxonomy of one isolate, strain MCS 33T, obtained from above the hot water plume of a deep-sea hydrothermal vent near Vancouver island, Canada. Cells contained no detectable phospholipids or sulpholipids, but did contain 1,2-di-O-acyl-3-O-α-d-glucopyranosylglycerol, 1,2-di-O-acyl-3-O-α-d-glucopyranuronosylglycerol and the novel lipid 1,2-di-O-acyl-3-[O-α-d-glucopyranuronosyl]glycerol-6′-N-glycine. It is assumed that the various glucoronosyl lipids are replacing, at least partially, the phospholipids in their various tasks in the cell cycle. The G+C content of the genomic DNA of strain MCS 33T was 62.8 mol%, and Q10 was the predominant respiratory ubiquinone. The 16S rRNA gene sequence of this chemoheterotrophic, aerobic, moderately halophilic strain showed only a low similarity of 94.4 % to that of Oceanicaulis alexandrii C116-18T, and both strains also differed based on their lipids. Although the novel strain was isolated from seawater sampled near a hydrothermal vent, its optimum temperature for growth was 30 °C. The main cellular fatty acids were C18 : 1ω7c, C18 : 0 and the unknown fatty acid ECL 11.798, and the main hydroxy fatty acid was C12 : 0 3-OH. The strain is proposed to represent a novel species of a new genus, Glycocaulis abyssi gen. nov., sp. nov. The type strain of the type species is MCS 33T ( = LMG 27140T = CCUG 62981T).

Brevundimonas abyssalis sp. nov., a dimorphic prosthecate bacterium isolated from deep-subsea floor sediment

A novel Gram-negative, aerobic, psychrotolerant, alkali-tolerant, heterotrophic and dimorphic prosthecate bacterium, designated strain TAR-001T, was isolated from deep-sea floor sediment in Japan. Cells of this strain had a dimorphic life cycle and developed an adhesive stalk at a site not coincident with the centre of the cell pole, and the other type of cell, a swarm cell, had a polar flagellum. Colonies were glossy, viscous and yellowish-white in colour. The temperature, pH and salt concentration range for growth were 2–41 °C, pH 6.5–10.0 and 1–4 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain TAR-001T belongs to the family Caulobacteraceae of the class Alphaproteobacteria , and lies between the genus Brevundimonas and the genus Caulobacter . Levels of similarity between the 16S rRNA gene sequence of strain TAR-001T and those of the type strains of Brevundimonas species were 93.3–95.7 %; highest sequence similarity was with the type strain of Brevundimonas diminuta . Levels of sequence similarity between those of the type strains of Caulobacter species were 94.9–96.0 %; highest sequence similarity was with the type strain of Caulobacter mirabilis . The G+C content of strain TAR-001T was 67.6 mol%. Q-10 was the major respiratory isoprenoid quinone. The major fatty acids were C18 : 1ω7c and C16 : 0, and the presence of 1,2-di-O-acyl-3-O-[d-glucopyranosyl-(1→4)-α-d-glucopyranuronosyl]glycerol suggests strain TAR-001T is more closely to the genus Brevundimonas than to the genus Caulobacter . The mean DNA–DNA hybridization levels between strain TAR-001T and the type strains of two species of the genus Brevundimonas were higher than that of the genus Caulobacter . On the basis of polyphasic biological features and the 16S rRNA gene sequence comparison presented here, strain TAR-001T is considered to represent a novel species of the genus Brevundimonas , for which the name Brevundimonas abyssalis sp. nov. is proposed; the type strain is TAR-001T ( = JCM 18150T = CECT 8073T).

Marinicauda pacifica gen. nov., sp. nov., a prosthecate alphaproteobacterium of the family Hyphomonadaceae isolated from deep seawater

A marine prosthecate bacterium, designated strain P-1 km-3T, was isolated from deep seawater from the Pacific. Cells of strain P-1 km-3T were Gram-stain-negative, aerobic, catalase- and oxidase-positive, dimorphic rods with a single polar prostheca or flagellum. The strain hydrolysed gelatin and grew at 6–40 °C (optimum, 30 °C) and with 0.5–12 % (w/v) NaCl (optimum, 2 %). Phylogenetic analysis of the 16S rRNA gene sequences revealed that strain P-1 km-3T belonged to the family Hyphomonadaceae in the class Alphaproteobacteria and represented a separate lineage, located between the genera Oceanicaulis and Woodsholea . Sequence similarities of strain P-1 km-3T with type strains of species of the genera Oceanicaulis and Woodsholea were 93.2–93.9 %. The predominant cellular fatty acids in strain P-1 km-3T were C18 : 1ω7c, C18 : 0, 11-methyl C18 : 1ω7c, C17 : 0 and C19 : 0 cyclo ω8c. The major respiratory quinone of strain P-1 km-3T was Q-10. The polar lipids of strain P-1 km-3T comprised glucuronopyranosyldiglyceride (GUDG), monoglycosyldiglyceride (MGDG), sulfo-quinovosyl diacylglycerol (SQDG), phosphatidylglycerol (PG), an unidentified phospholipid (PL) and an unidentified lipid (L). The genomic DNA G+C content of strain P-1 km-3T was 66.0 mol%. On the basis of the polyphasic data presented in this study, strain P-1 km-3T is proposed to represent a novel species in a new genus, Marinicauda pacifica gen. nov., sp. nov., within the family Hyphomonadaceae . The type strain of the type species is P-1 km-3T ( = KACC 16526T = CGMCC 1.11031T).

Oceanicaulis stylophorae sp. nov., isolated from the reef-building coral Stylophora pistillata

A bacterial strain designated GISW-4T was isolated from the reef-building coral Stylophora pistillata, collected from seawater off the coast of southern Taiwan, and was characterized in this taxonomic study using a polyphasic approach. Strain GISW-4T was Gram-stain-negative, aerobic, beige, rod-shaped, and dimorphic, either non-motile with stalks (or prosthecae), or non-stalked and motile by means of a single polar flagellum. 16S rRNA gene sequence studies showed that the novel strain clustered with Oceanicaulis alexandrii C116-18T (98.9 % 16S rRNA gene sequence similarity). Strain GISW-4T exhibited optimal growth at 35–40 °C, 1–2 % (w/v) NaCl and at pH 7–9. The predominant cellular fatty acids (>10 %) were C18 : 0, C18 : 1ω7c and C18 : 1ω7c 11-methyl. The predominant polar lipids were phosphatidylglycerol, sulfoquinovosyl diacylglycerol and two unknown phospholipids (PL1–2). The major respiratory quinones were ubiquinone Q-10 and Q-9, and the DNA G+C content was 61.6 mol%. The results of physiological and biochemical tests allowed clear phenotypic differentiation of strain GISW-4T from the type strain of O. alexandrii . It is evident from the genotypic, phenotypic and chemotaxonomic data that the isolate should be classified as a novel species of the genus Oceanicaulis . The name proposed for this taxon is Oceanicaulis stylophorae sp. nov., with the type strain GISW-4T ( = LMG 25723T = BCRC 80207T).

Genome sequence of Oceanicaulis sp. strain HTCC2633, isolated from the Western Sargasso Sea

The genus Oceanicaulis represents dimorphic rods that were originally isolated from a marine dinoflagellate. Here, we announce the genome sequence of Oceanicaulis sp. strain HTCC2633, isolated by dilution-to-extinction culturing from the Sargasso Sea. The genome information of strain HTCC2633 indicates a chemoorganotrophic way of life of this strain.

Hellea balneolensis gen. nov., sp. nov., a prosthecate alphaproteobacterium from the Mediterranean Sea

A novel aerobic, heterotrophic, prosthecate bacterium, designated 26III/A02/215(T), was isolated from surface water of the north-western Mediterranean Sea. Cells stained Gram-negative and were straight to slightly curved rods, forming red colonies on agar plates. The strain grew at 15-37 degrees C inclusive (optimum 30 degrees C) and grew optimally at seawater salinity. Growth was observed on organic acids, amino acids and complex organic substrates. The fatty acids (>5 %) detected in strain 26III/A02/215(T) were C(17 : 1)omega6c, C(18 : 1)omega7c and C(17 : 0). The lipid pattern indicated the presence of phosphatidylglycerol, glucuronopyranosyldiglyceride, monoglycosyldiglyceride, an unidentified glycolipid and three unidentified phospholipids. Phosphatidylethanolamine and diphosphatidylglycerol were absent. Ubiquinone Q-10 was the only respiratory lipoquinone. The G+C content of the genomic DNA was 46.8 mol%. Comparative 16S rRNA gene sequence analysis indicated that strain 26III/A02/215(T) belonged to the Hyphomonas-Hirschia-Robiginitomaculum branch of the order Caulobacterales. This affiliation was consistent with the results of polar lipid analyses. Among this group, the novel isolate was most closely related to Robiginitomaculum antarcticum (93.9 % 16S rRNA gene sequence similarity to the type strain). On the basis of genotypic, chemotaxonomic and phenotypic distinctness, we propose a novel genus, Hellea gen. nov., with Hellea balneolensis sp. nov. as the type species. The type strain of Hellea balneolensis is 26III/A02/215(T) (=DSM 19091(T) =CIP 109500(T) =OOB 269(T)).

Metagenomic and stable isotopic analyses of modern freshwater microbialites in Cuatro Ciénegas, Mexico

Ancient biologically mediated sedimentary carbonate deposits, including stromatolites and other microbialites, provide insight into environmental conditions on early Earth. The primary limitation to interpreting these records is our lack of understanding regarding microbial processes and the preservation of geochemical signatures in contemporary microbialite systems. Using a combination of metagenomic sequencing and isotopic analyses, this study describes the identity, metabolic potential and chemical processes of microbial communities from living microbialites from Cuatro Ciénegas, Mexico. Metagenomic sequencing revealed a diverse, redox-dependent microbial community associated with the microbialites. The microbialite community is distinct from other marine and freshwater microbial communities, and demonstrates extensive environmental adaptation. The microbialite metagenomes contain a large number of genes involved in the production of exopolymeric substances and the formation of biofilms, creating a complex, spatially structured environment. In addition to the spatial complexity of the biofilm, microbial activity is tightly controlled by sensory and regulatory systems, which allow for coordination of autotrophic and heterotrophic processes. Isotopic measurements of the intracrystalline organic matter demonstrate the importance of heterotrophic respiration of photoautotrophic biomass in the precipitation of calcium carbonate. The genomic and stable isotopic data presented here significantly enhance our evolving knowledge of contemporary biomineralization processes, and are directly applicable to studies of ancient microbialites.

Structure and function of glycoglycerolipids in plants and bacteria

Phosphoglycerolipids are abundant membrane constituents in prokaryotic and eukaryotic cells. However, glycoglycerolipids are the predominant lipids in chloroplasts of plants and eukaryotic algae and in cyanobacteria. Membrane composition in chloroplasts and cyanobacteria is highly conserved, with monogalactosyldiacylglycerol (MGD) and digalactosyldiacylglycerol (DGD) representing the most abundant lipids. The genes encoding enzymes of galactolipid biosynthesis have been isolated from Arabidopsis. Galactolipids are crucial for growth under normal and phosphate limiting conditions. Furthermore, they are indispensable for maximal efficiency of photosynthesis. A wide variety of glycoglycerolipids is found in different bacteria. These lipids contain glucose or galactose, in some cases also mannose or other sugars with different glycosidic linkages in their head group. Some bacterial species produce unusual glycoglycerolipids, such as glycophospholipids or glycoglycerolipids carrying sugar head groups esterified with acyl residues. A number of genes coding for bacterial glycoglycerolipid synthases have been cloned and the enzymes characterized. In contrast to the breadth of information available on their structural diversity, much less is known about functional aspects of bacterial glycoglycerolipids. In some bacteria, glycoglycerolipids are required for membrane bilayer stability, they serve as precursors for the formation of complex membrane components, or they are crucial to support anoxygenic photosynthesis or growth during phosphate deficiency.

Sulfolipids dramatically decrease phosphorus demand by picocyanobacteria in oligotrophic marine environments

There is growing evidence that dissolved phosphorus can regulate planktonic production in the oceans' subtropical gyres, yet there is little quantitative information about the biochemical fate of phosphorus in planktonic communities. We observed in the North Pacific Subtropical Gyre (NPSG) that the synthesis of membrane lipids accounted for 18-28% of the phosphate (PO4(3-)) taken up by the total planktonic community. Paradoxically, Prochlorococcus, the cyanobacterium that dominates NPSG phytoplankton, primarily synthesizes sulfoquinovosyldiacylglycerol (SQDG), a lipid that contains sulfur and sugar instead of phosphate. In axenic cultures of Prochlorococcus, it was observed that <1% of the total PO4(3-) uptake was incorporated into membrane lipids. Liquid chromatography/mass spectrometry of planktonic lipids in the NPSG confirmed that SQDG was the dominant membrane lipid. Furthermore, the analyses of SQDG synthesis genes from the Sargasso Sea environmental genome showed that the use of sulfolipids in subtropical gyres was confined primarily to picocyanobacteria; no sequences related to known heterotrophic bacterial SQDG lineages were found. This biochemical adaptation by Prochlorococcus must be a significant benefit to these organisms, which compete against phospholipid-rich heterotrophic bacteria for PO4(3-). Thus, evolution of this "sulfur-for-phosphorus" strategy set the stage for the success of picocyanobacteria in oligotrophic environments and may have been a major event in Earth's early history when the relative availability of sulfate and PO4(3-) were significantly different from today's ocean.

Identification of sulfoquinovosyl diacylglycerol as a major polar lipid in Marinococcus halophilus and Salinicoccus hispanicus and substitution with phosphatidylglycerol

The sulfonolipid sulfoquinovosyl diacylglycerol normally associated with photosynthetic membranes was identified as a major lipid in Marinococcus halophilus, Salinicoccus hispanicus ("Marinococcus hispanicus"), and Marinococcus sp. H8 (Planococcus sp. H8). Phosphatidylglycerol and 0%–10% cardiolipin accounted for the remaining polar lipids in these moderately halophilic, Gram-positive bacteria. Negative-ion fast atom bombardment mass spectrometry was used to quantify these three polar lipids from cells grown in media containing 0.03 to 4 mol NaCl/L. All strains revealed dramatic shifts in the ratio of sulfonolipid to phospholipid dependent on the salinity of the growth media, when grown in media with low phosphate content. Highest sulfonolipid content occurred during best growth in 0.5–2 mol NaCl/L, approaching 80%–90% of the total polar lipids. It was demonstrated that growth of M. halophilus in the presence of elevated phosphate and low sulfate blocked the shift to decreased phospholipids most notably during growth in 0.5–2 mol NaCl/L, without significant influence on growth. The data suggest that in low-phosphate media the influence of NaCl concentration on growth rate (and resulting demand for phosphate by competing pathways) is the primary factor responsible for exchange between phospholipid and sulfonolipid. We conclude that sulfoquinovosyl diacylglycerol, by substitution with phospholipids, contributes to the ability of these Gram-positive cocci to adapt to changing ionic environments. A comparison of 16S rRNA established a close similarity between Planococcus sp. H8 and M. halophilus.Key words: sulfoquinovosyl diacylglycerol, salinity, Marinococcus halophilus, Salinicoccus hispanicus, Marinococcus sp. H8 (Planococcus sp. H8).

Thalassobius mediterraneus gen. nov., sp. nov., and reclassification of Ruegeria gelatinovorans as Thalassobius gelatinovorus comb. nov

A Gram-negative, slightly halophilic, non-pigmented, strictly aerobic, chemo-organotrophic bacterium was isolated from sea water off the western Mediterranean coast near Valencia (Spain). This strain was able to grow on several organic acids and amino acids added to a minimal medium as carbon sources, but used few carbohydrates or yielded slight growth when sugars were used. Phylogenetic analysis based on an almost complete 16S rRNA gene sequence revealed that strain XSM19T was a member of the Roseobacter group within the 'Alphaproteobacteria', with its closest phylogenetic neighbour being Ruegeria gelatinovorans (97.6 % sequence similarity). Following a polyphasic approach, it was concluded that strain XSM19T represents a new genus and novel species, for which the name Thalassobius mediterraneus sp. nov. is proposed. The type strain is XSM19T (=CECT 5383T=CIP 108400T=CCUG 49438T). It is also proposed that R. gelatinovorans (Rüger & Höfle 1992) Uchino et al. 1999 is reclassified as Thalassobius gelatinovorus comb. nov.