Stable Isotope Probing-nanoFTIR for Quantitation of Cellular Metabolism and Observation of Growth-Dependent Spectral Features.

This study utilizes nanoscale Fourier transform infrared spectroscopy (nanoFTIR) to perform stable isotope probing (SIP) on individual bacteria cells cultured in the presence of 13C-labelled glucose. SIP-nanoFTIR simultaneously quantifies single-cell metabolism through infrared spectroscopy and acquires cellular morphological information via atomic force microscopy. The redshift of the amide I peak corresponds to the isotopic enrichment of newly synthesized proteins. These observations of single-cell translational activity are comparable to those of conventional methods, examining bulk cell numbers. Observing cells cultured under conditions of limited carbon, SIP- nanoFTIR is used to identify environmentally-induced changes in metabolic heterogeneity and cellular morphology. Individuals outcompeting their neighboring cells will likely play a disproportionately large role in shaping population dynamics during adverse conditions or environmental fluctuations. Additionally, SIP-nanoFTIR enables the spectroscopic differentiation of specific cellular growth phases. During cellular replication, subcellular isotope distribution becomes more homogenous, which is reflected in the spectroscopic features dependent on the extent of 13C-13C mode coupling or to specific isotopic symmetries within protein secondary structures. As SIP-nanoFTIR captures single-cell metabolism, environmentally-induced cellular processes, and subcellular isotope localization, this technique offers widespread applications across a variety of disciplines including microbial ecology, biophysics, biopharmaceuticals, medicinal science, and cancer research.

The polar lipids of Clostridium psychrophilum, an anaerobic psychrophile.

We have examined the polar lipids of Clostridium psychrophilum, a recently characterized psychrophilic Clostridium isolated from an Antarctic microbial mat. Lipids were extracted from cells grown near the optimal growth temperature (+5°C) and at -5°C, and analyzed by two-dimensional thin layer chromatography and liquid chromatography coupled with mass spectrometry. The major phospholipids of this species are: cardiolipin, phosphatidylethanolamine, and phosphatidylglycerol. Phosphatidylserine and lyso-phosphatidylethanolamine were found as minor components. The most abundant glycolipids are a monoglycosyldiradylglycerol (MGDRG) and a diglycosyldiradylglycerol (DGDRG). The latter was only seen in cells grown at -5°C. An ethanolamine-phosphate derivative of N-acetylglucosaminyldiradylglycerol was seen in cells grown at -5°C and an ethanolamine-phosphate derivative of MGDRG was found in cells grown at +5°C. All lipids were present in both the all acyl and plasmalogen (alk-1'-enyl acyl) forms with the exception of PS and MGDRG, which were predominantly in the diacyl form. The significance of lipid changes at the two growth temperatures is discussed.

Influence of calcium ions on rhamnolipid and rhamnolipid/anionic surfactant adsorption and self-assembly.

The impact of Ca(2+) counterions on the adsorption at the air-water interface and self-assembly in aqueous solution of the rhamnolipid biosurfactant and its mixture with the anionic surfactant sodium dodecylbenzenesulfonate, LAS, has been studied using neutron reflectometry and small-angle neutron scattering. The results illustrate how rhamnolipids are calcium tolerant and how their blending with conventional anionic surfactants improves the calcium tolerance of the anionic surfactant. Ca(2+) has relatively little effect upon the adsorption and self-assembly of the monorhamnose, R1, and dirhamnose, R2, rhamnolipids, even at high pH, due to their predominantly nonionic nature. For R1/R2 mixtures the addition of Ca(2+) has little impact upon the adsorbed amount or the surface composition. For R2/LAS mixtures the addition of Ca(2+) results in an increased adsorption and a surface slightly richer in R2. The weak binding of Ca(2+) to R1 and R2 does result in a change to the degree of ionization of the micelles and especially for mixed R1/R2 micelles at R1-rich solution compositions. The stronger binding of Ca(2+) to LAS results in the addition of Ca(2+) having a much greater impact on the self-assembly of R1/LAS and R2/LAS mixtures. For R1/LAS mixtures the addition of Ca(2+) promotes the formation of more planar structures, even at low surfactant concentrations where in the absence of Ca(2+) mixed globular micelle formation dominates. In R2/LAS mixtures, where there is a greater contrast between the high and low preferred curvatures associated with R2 and LAS, the addition of Ca(2+) results in a more complex evolution in micellar aggregation and the degree of ionization of the micelles. This results in variations in Ca(2+) binding that promotes micellar structures in which a spatial segregation of the two surfactant components within the micelle occurs.

Rhamnolipids are conserved biosurfactants molecules: implications for their biotechnological potential.

A range of isolates of Pseudomonas aeruginosa from widely different environmental sources were examined for their ability to synthesise rhamnolipid biosurfactants. No significant differences in the quantity or composition of the rhamnolipid congeners could be produced by manipulating the growth conditions. Sequences for the rhamnolipid genes indicated low levels of strain variation, and the majority of polymorphisms did lead to amino acid sequence changes that had no evident phenotypic effect. Expression of the rhlB and rhlC rhamnosyltransferase genes showed a fixed sequential expression pattern during growth, and no significant up-regulation could be induced by varying producer strains or growth media. The results indicated that rhamnolipids are highly conserved molecules and that their gene expression has a rather stringent control. This leaves little opportunity to manipulate and greatly increase the yield of rhamnolipids from strains of P. aeruginosa for biotechnological applications.

Low-Temperature Microbiology Meets the Global Challenges of Our Time.

Low-temperature microbiology is intimately associated with the exploration of the polar regions, and research in recent decades has focused on characterizing the microbial biodiversity of the cryosphere [...].

Adsorption of sophorolipid biosurfactants on their own and mixed with sodium dodecyl benzene sulfonate, at the air/water interface.

The adsorption of the lactonic (LS) and acidic (AS) forms of sophorolipid and their mixtures with the anionic surfactant sodium dodecyl benzene sulfonate (LAS) has been measured at the air/water interface by neutron reflectivity, NR. The AS and LS sophorolipids adsorb with Langmuir-like adsorption isotherms. The more hydrophobic LS is more surface active than the AS, with a lower critical micellar concentration, CMC, and stronger surface adsorption, with an area/molecule ∼70 Å(2) compared with 85 Å(2) for the AS. The acidic sophorolipid shows a maximum in its adsorption at the CMC which appears to be associated with a mixture of different isomeric forms. The binary LS/AS and LS/LAS mixtures show a strong surface partitioning in favor of the more surface active and hydrophobic LS component but are nevertheless consistent with ideal mixing at the interface. In contrast, the surface composition of the AS/LAS mixture is much closer to the solution composition, but the surface mixing is nonideal and can be accounted for by regular solution theory, RST. In the AS/LS/LAS ternary mixtures, the surface adsorption is dominated by the sophorolipid, and especially the LS component, in a way that is not consistent with the observations for the binary mixtures. The extreme partitioning in favor of the sophorolipid for the LAS/LS/AS (1:2) mixtures is attributed to a reduction in the packing constraints at the surface due to the AS component. Measurements of the surface structure reveal a compact monolayer for LS and a narrow solvent region for LS, LS/AS, and LS/LAS mixtures, consistent with the more hydrophobic nature of the LS component. The results highlight the importance of the relative packing constraints on the adsorption of multicomponent mixtures, and the impact of the lactonic form of the sophorolipid on the adsorption of the sophorolipid/LAS mixtures.

Solution self-assembly of the sophorolipid biosurfactant and its mixture with anionic surfactant sodium dodecyl benzene sulfonate.

The self-assembly in aqueous solution of the acidic (AS) and lactonic (LS) forms of the sophorolipid biosurfactant, their mixtures, and their mixtures with anionic surfactant sodium dodecyl benzene sulfonate, LAS, has been studied using predominantly small-angle neutron scattering, SANS, at relatively low surfactant concentrations of <30 mM. The more hydrophobic lactonic sophorolipid forms small unilamellar vesicles at low surfactant concentrations, in the concentration range of 0.2 to 3 mM, and transforms via a larger unilamellar vesicle structure at 7 mM to a disordered dilute phase of tubules at higher concentrations, 10 to 30 mM. In marked contrast, the acidic sophorolipid is predominantly in the form of small globular micelles in the concentration range of 0.5 to 30 mM, with a lower concentration of larger, more planar aggregates (lamellar or vesicular) in coexistence. In mixtures of AS and LS, over the same concentration range, the micellar structure associated with the AS sophorolipid dominates the mixed-phase behavior. In mixtures of anionic surfactant LAS with the AS sophorolipid, the globular micellar structure dominates over the entire composition and concentration range studied. In contrast, mixtures of LAS with the LS sophorolipid exhibit a rich evolution in phase behavior with solution composition and concentration. At low surfactant concentrations, the small unilamellar vesicle structure present for LS-rich solution compositions evolves into a globular micelle structure as the solution becomes richer in LAS. At higher surfactant concentrations, the disordered lamellar structure present for LS-rich compositions transforms to small vesicle/lamellar coexistence, to lamellar/micellar coexistence, to micellar/lamellar coexistence, and ultimately to a pure micellar phase as the solution becomes richer in LAS. The AS sophorolipid surfactant exhibits self-assembly properties similar to those of most other weakly ionic or nonionic surfactants that have relatively large headgroups. However, the more hydrophobic nature of the lactonic sophorolipid results in a more complex and unusual evolution in phase behavior with concentration and with concentration and composition when mixed with anionic surfactant LAS.

Directed microbial biosynthesis of deuterated biosurfactants and potential future application to other bioactive molecules.

Deuterated rhamnolipids were produced using strain AD7 of Pseudomonas aeruginosa, which was progressively adapted to increasing levels of deuterium in D(2)O and carbon substrates. Fourteen different deuterated rhamnolipid structures, including structural isomers, were produced which is similar to normal protonated structures. There were two main products monorhamnolipid Rha-C(10)-C(10) and dirhamnolipid Rha(2)-C(10)-C(10). The levels of deuteration varied from 16% with 25% D(2)O + h-glycerol to 90% with 100% D(2)O + d-glycerol. When d-tetradecane was used with H(2)O, virtually all the deuterium appeared in the lipid chains while using h-tetradecane + D(2)O led to the majority of deuterium in the sugars. The adaptation to growth in deuterium appeared to be metabolic since no genetic changes could be found in the key rhamnolipid biosynthetic genes, the rhamnosyl transferases RhlB and RhlC. Deuterated sophorolipids were similarly produced using Candida bombicola and Candida apicola although in this case, no adaptation process was necessary. Up to 40 different sophorolipids were produced by these yeasts. However, unlike the rhamnolipids, use of D(2)O did not lead to any deuteration of the lipid chains, but direct incorporation into the lipid was achieved using d-isostearic acid. The results from these experiments show the feasibility of producing deuterated bioactive compounds from microorganisms coupled with the possibility of manipulating the pattern of labelling through judicious use of different deuterated substrates.

Possibilities and challenges for biosurfactants use in petroleum industry.

Biosurfactants are a group of microbial molecules identified by their unique capabilities to interact with hydrocarbons. Emulsification and de-emulsification, dispersion, foaming, wetting and coating are some of the numerous surface activities that biosurfactants can achieve when applied within systems such as immiscible liquid/liquid (e.g., oil/water), solid/ liquid (e.g., rock/oil and rock/water) and gas/liquid. Therefore, the possibilities of exploiting these bioproducts in oil-related sciences are vast and made petroleum industry their largest possible market at present. The role of biosurfactants in enhancing oil recovery from reservoirs is certainly the best known; however they can be effectively applied in many other fields from transportation of crude oil in pipeline to the clean-up of oil storage tanks and even manufacturing of fine petrochemicals. When properly used, biosurfactants are comparable to traditional chemical analogues in terms of performances and offer advantages with regard to environment protection/conservation. This chapter aims at providing an up-to-date overview of biosurfactant roles, applications and possible future uses related to petroleum industry.

Discovery and Characterization of a New Cold-Active Protease From an Extremophilic Bacterium via Comparative Genome Analysis and in vitro Expression.

Following a screening of Antarctic glacier forefield-bacteria for novel cold-active enzymes, a psychrophilic strain Psychrobacter sp. 94-6PB was selected for further characterization of enzymatic activities. The strain produced lipases and proteases in the temperature range of 4-18°C. The coding sequence of an extracellular serine-protease was then identified via comparative analysis across Psychrobacter sp. genomes, PCR-amplified in our strain 94-6PB and expressed in the heterologous host E. coli. The purified enzyme (80 kDa) resulted to be a cold-active alkaline protease, performing best at temperatures of 20-30°C and pH 7-9. It was stable in presence of common inhibitors [ß-mercaptoethanol (ß-ME), dithiothreitol (DTT), urea, phenylmethylsulfonyl fluoride (PMSF) and ethylenediaminetetraacetic acid (EDTA)] and compatible with detergents and surfactants (Tween 20, Tween 80, hydrogen peroxide and Triton X-100). Because of these properties, the P94-6PB protease may be suitable for use in a new generation of laundry products for cold washing. Furthermore, we assessed the microdiversity of this enzyme in Psychrobacter organisms from different cold habitats and found several gene clusters that correlated with specific ecological niches. We then discussed the role of habitat specialization in shaping the biodiversity of proteins and enzymes and anticipate far-reaching implications for the search of novel variants of biotechnological products.

Going Green and Cold: Biosurfactants from Low-Temperature Environments to Biotechnology Applications.

Approximately 80% of the Earth's biosphere is cold, at an average temperature of 5°C, and is populated by a diversity of microorganisms that are a precious source of molecules with high biotechnological potential. Biosurfactants from cold-adapted organisms can interact with multiple physical phases - water, ice, hydrophobic compounds, and gases - at low and freezing temperatures and be used in sustainable (green) and low-energy-impact (cold) products and processes. We review the biodiversity of microbial biosurfactants produced in cold habitats and provide a perspective on the most promising future applications in environmental and industrial technologies. Finally, we encourage exploring the cryosphere for novel types of biosurfactants via both culture screening and functional metagenomics.

Thermally enhanced approaches for bioremediation of hydrocarbon-contaminated soils.

Successful remediation of contaminated soils is often limited by the low bioavailability of hydrophobic pollutants, which may slow the process significantly. In this study we investigated the benefits of high temperature in enhancing hydrocarbon degradation rates and evaluated the effect of different biostimulants. Hexadecane polluted soil microcosms with various amendments were incubated both at 60 degrees C and room temperature (18 degrees C) and analyzed periodically up to 40d for the degradation of hydrocarbon and the response of the microbial population. Natural attenuation showed a satisfactory intrinsic degradative capability at 60 degrees C and the addition of inorganic N, P and K increased the degradation rates by 10%. The addition of rhamnolipid biosurfactant further enhanced the bioavailability of alkane to microbial degradation resulting in up to 71% removal at 60 degrees C and 42% at 18 degrees C. Significant input to hexadecane degradation occurred at 60 degrees C (70%) as a result of the bioaugmentation with thermophilic Geobacillus thermoleovorans T80, which did not take place at 18 degrees C. Coupling high temperature to all amendments resulted in 90% removal of the hexadecane from soil after 40d which was also accompanied with an increase in bacterial numbers. The results suggest that thermally enhanced bioremediation may be an efficient technology for the treatment of hydrocarbon-contaminated soils.

The degradation of n-hexadecane in soil by thermophilic geobacilli.

Soil microcosms have been used to demonstrate the ability of indigenous soil thermophiles to degrade effectively a representative alkane (n-hexadecane). A fragment of the alkane mono-oxygenase gene (alkB) was amplified from thermophilic Geobacillus thermoleovorans strain T70 by PCR using degenerate primers. The amplicon demonstrated 96% sequence similarity with the alkB gene from Rhodococcus erythropolis. Critical controls ensured that the positive PCR signal detected was not a result of mesophilic soil organisms. A reverse transcription PCR (RT-PCR) assay was developed to determine if expression of the gene was inducible in the presence of an alkane or constitutively expressed in soil. In the presence of n-hexadecane, expression of the alkane mono-oxygenase gene was induced in pure cultures and soil samples and was dependent on temperature. No positive RT-PCR signal was detected at mesophilic growth temperatures either in pure cultures or in soil microcosms, whereas at 55 degrees C positive RT-PCR signals were obtained for both pure cultures of T70 and soil samples. Many different amplicons of the alkB gene fragment were obtained from the soil used in the microcosms. Thirty cloned fragments yielded 27 different sequences showing 85-96% sequence similarity with the alkB sequence of T70. To establish that the amplified alkB gene sequences from soil were derived from thermophilic geobacilli, additional strains were isolated on a selective medium containing n-hexadecane as sole carbon source. The 16S rRNA gene sequences were determined to identify the 50 isolates obtained (G. thermoleovorans, 27; G. caldoxylosilyticus, 17; G. pallidus, 2; G. toebiii, 1; Geobacillus sp., 3) representing 18 different strains and alkB gene sequences determined and deposited with the European Bioinformatics Institute.

Hydrocarbon degraders establish at the costs of microbial richness, abundance and keystone taxa after crude oil contamination in permafrost environments.

Oil spills from pipeline ruptures are a major source of terrestrial petroleum pollution in cold regions. However, our knowledge of the bacterial response to crude oil contamination in cold regions remains to be further expanded, especially in terms of community shifts and potential development of hydrocarbon degraders. In this study we investigated changes of microbial diversity, population size and keystone taxa in permafrost soils at four different sites along the China-Russia crude oil pipeline prior to and after perturbation with crude oil. We found that crude oil caused a decrease of cell numbers together with a reduction of the species richness and shifts in the dominant phylotypes, while bacterial community diversity was highly site-specific after exposure to crude oil, reflecting different environmental conditions. Keystone taxa that strongly co-occurred were found to form networks based on trophic interactions, that is co-metabolism regarding degradation of hydrocarbons (in contaminated samples) or syntrophic carbon cycling (in uncontaminated samples). With this study we demonstrate that after severe crude oil contamination a rapid establishment of endemic hydrocarbon degrading communities takes place under favorable temperature conditions. Therefore, both endemism and trophic correlations of bacterial degraders need to be considered in order to develop effective cleanup strategies.

Epifluorescence, SEM, TEM and nanoSIMS image analysis of the cold phenotype of Clostridium psychrophilum at subzero temperatures.

We have applied an image-based approach combining epifluorescence microscopy, electron microscopy and nanoscale secondary ion mass spectrometry (nanoSIMS) with stable isotope probing to examine directly the characteristic cellular features involved in the expression of the cold phenotype in the Antarctic bacterium Clostridium psychrophilum exposed to a temperature range from +5 to -15 °C under anoxic conditions. We observed dramatic morphological changes depending on temperature. At temperatures below -10 °C, cell division was inhibited and consequently filamentous growth predominated. Bacterial cells appeared surrounded by a remarkably thick cell wall and a capsule formed of long exopolysaccharide fibres. Moreover, bacteria were entirely embedded within a dense extracellular matrix, suggesting a role both in cryo-protection and in the cycling of nutrients and genetic material. Strings of extracellular DNA, transient cell membrane permeability and release of membrane vesicles were observed that suggest that evolution via transfer of genetic material may be especially active under frozen conditions. While at -5 °C, the bacterial population was metabolically healthy, at temperatures below -10 °C, most cells showed no sign of active metabolism or the metabolic flux was extremely slowed down; instead of being consumed, carbon was accumulated and stored in intracellular granules as in preparation for a long-term survival.

Microbial diversity in Calamita ferromagnetic sand.

Calamita is a black ferromagnetic sand from a marine iron ore on Elba Island (Italy). Its total iron content is approximately 80% and a major fraction (63% w/w) has magnetic properties. Desiccation, ultraviolet irradiation and the high temperature induced by the thermal conductivity of iron make Calamita sand an extreme biotope. We report, for the first time, the geomicrobiological characterization of Calamita sand, which showed a low bacterial biodiversity as determined by denaturing gradient gel electrophoresis and 16S rRNA gene clone library analysis. We retrieved sequences closely affiliated with uncultured bacteria inhabiting the harshest deserts on Earth. Radiation- and desiccation-tolerant bacteria from the phyla Proteobacteria, Actinobacteria and Deinococcus-Thermus dominated the community. Heavy metal-resistant organisms, for example Variovorax sp. were also abundant. Sequences of organisms with an inferred metabolism based on lithotrophic iron oxidation were detected. The sands also contained thermophilic bacilli, which were cultivated at 60°C. These data provided important insights also into the biogeographical distribution of these organisms in the Mediterranean region. In summary, this study on Calamita helps to expand our knowledge of the biodiversity in extreme, iron-rich, environments.

Global transport of thermophilic bacteria in atmospheric dust.

Aerosols from dust storms generated in the Sahara-Sahel desert area of Africa are transported north over Europe and periodically result in dry dust precipitation in the Mediterranean region. Samples of dust collected in Turkey and Greece following two distinct desert storm events contained viable thermophilic organisms of the genus Geobacillus, namely G. thermoglucosidasius and G. thermodenitrificans, and the recently reclassified Aeribacillus pallidus (formerly Geobacillus pallidus). We present here evidence that African dust storms create an atmospheric bridge between distant geographical regions and that they are also probably the source of thermophilic geobacilli later deposited over northern Europe by rainfall or dust plumes themselves. The same organisms (99% similarity in the 16S rDNA sequence) were found in dust collected in the Mediterranean region and inhabiting cool soils in Northern Ireland. This study also contributes new insights to the taxonomic identification of Geobacillus sp. Attempts to identify these organisms using 16S rRNA gene sequences have revealed that they contain multiple and diverse copies of the ribosomal RNA operon (up to 10 copies with nine different sequences), which dictates care in interpreting data about the systematics of this genus.

Rhamnolipid production by a novel thermophilic hydrocarbon-degrading Pseudomonas aeruginosa AP02-1.

Thermophilic bacterial cultures were isolated from a hot spring environment on hydrocarbon containing mineral salts media. One strain identified as Pseudomonas aeruginosa AP02-1 was tested for the ability to utilize a range of hydrocarbons both n-alkanes and polycyclic aromatic hydrocarbons as sole carbon source. Strain AP02-1 had an optimum growth temperature of 45 degrees C and degraded 99% of crude oil 1% (v/v) and diesel oil 2% (v/v) when added to a basal mineral medium within 7 days of incubation. Surface activity measurements indicated that biosurfactants, mainly glycolipid in nature, were produced during the microbial growth on hydrocarbons as well as on both water-soluble and insoluble substrates. Mass spectrometry analysis showed different types of rhamnolipid production depending on the carbon substrate and culture conditions. Grown on glycerol, P. aeruginosa AP02-1 produced a mixture of ten rhamnolipid homologues, of which Rha-Rha-C10-C10 and Rha-C10-C10 were predominant. Rhamnolipid-containing culture broths reduced the surface tension to approximately 28 mN and gave stable emulsions with a number of hydrocarbons and remained effective after sterilization. Microscopic observations of the emulsions suggested that hydrophobic cells acted as emulsion-stabilizing agents.