Genome analysis and characterisation of the exopolysaccharide produced by Bifidobacterium longum subsp. longum 35624™

The Bifibobacterium longum subsp. longum 35624™ strain (formerly named Bifidobacterium longum subsp. infantis) is a well described probiotic with clinical efficacy in Irritable Bowel Syndrome clinical trials and induces immunoregulatory effects in mice and in humans. This paper presents (a) the genome sequence of the organism allowing the assignment to its correct subspeciation longum; (b) a comparative genome assessment with other B. longum strains and (c) the molecular structure of the 35624 exopolysaccharide (EPS624). Comparative genome analysis of the 35624 strain with other B. longum strains determined that the sub-speciation of the strain is longum and revealed the presence of a 35624-specific gene cluster, predicted to encode the biosynthetic machinery for EPS624. Following isolation and acid treatment of the EPS, its chemical structure was determined using gas and liquid chromatography for sugar constituent and linkage analysis, electrospray and matrix assisted laser desorption ionization mass spectrometry for sequencing and NMR. The EPS consists of a branched hexasaccharide repeating unit containing two galactose and two glucose moieties, galacturonic acid and the unusual sugar 6-deoxy-L-talose. These data demonstrate that the B. longum 35624 strain has specific genetic features, one of which leads to the generation of a characteristic exopolysaccharide.

Real time analysis of atmospheric single particles in urban environments using aerosol time of flight mass spectrometry

In order to determine the size-resolved chemical composition of single particles in real-time an ATOFMS was deployed at urban background sites in Paris and Barcelona during the MEGAPOLI and SAPUSS monitoring campaigns respectively. The particle types detected during MEGAPOLI included several carbonaceous species, metal-containing types and sea-salt. Elemental carbon particle types were highly abundant, with 86% due to fossil fuel combustion and 14% attributed to biomass burning. Furthermore, 79% of the EC was apportioned to local emissions and 21% to continental transport. The carbonaceous particle types were compared with quantitative measurements from other instruments, and while direct correlations using particle counts were poor, scaling of the ATOFMS counts greatly improved the relationship. During SAPUSS carbonaceous species, sea-salt, dust, vegetative debris and various metal-containing particle types were identified. Throughout the campaign the site was influenced by air masses altering the composition of particles detected. During North African air masses the city was heavily influenced by Saharan dust. A regional stagnation was also observed leading to a large increase in carbonaceous particle counts. While the ATOFMS provides a list of particle types present during the measurement campaigns, the data presented is not directly quantitative. The quantitative response of the ATOFMS to metals was examined by comparing the ion signals within particle mass spectra and to hourly mass concentrations of; Na, K, Ca, Ti, V, Cr, Mn, Fe, Zn and Pb. The ATOFMS was found to have varying correlations with these metals depending on sampling issues such as matrix effects. The strongest correlations were observed for Al, Fe, Zn, Mn and Pb. Overall the results of this work highlight the excellent ability of the ATOFMS in providing composition and mixing state information on atmospheric particles at high time resolution. However they also show its limitations in delivering quantitative information directly.

Characterization of urban aerosol in Cork city (Ireland) using aerosol mass spectrometry

Ambient wintertime background urban aerosol in Cork city, Ireland, was characterized using aerosol mass spectrometry. During the three-week measurement study in 2009, 93% of the ca. 1 350 000 single particles characterized by an Aerosol Time-of-Flight Mass Spectrometer (TSI ATOFMS) were classified into five organic-rich particle types, internally mixed to different proportions with elemental carbon (EC), sulphate and nitrate, while the remaining 7% was predominantly inorganic in nature. Non-refractory PM1 aerosol was characterized using a High Resolution Time-of-Flight Aerosol Mass Spectrometer (Aerodyne HR-ToF-AMS) and was also found to comprise organic aerosol as the most abundant species (62 %), followed by nitrate (15 %), sulphate (9 %) and ammonium (9 %), and chloride (5 %). Positive matrix factorization (PMF) was applied to the HR-ToF-AMS organic matrix, and a five-factor solution was found to describe the variance in the data well. Specifically, "hydrocarbon-like" organic aerosol (HOA) comprised 20% of the mass, "low-volatility" oxygenated organic aerosol (LV-OOA) comprised 18 %, "biomass burning" organic aerosol (BBOA) comprised 23 %, non-wood solid-fuel combustion "peat and coal" organic aerosol (PCOA) comprised 21 %, and finally a species type characterized by primary m/z peaks at 41 and 55, similar to previously reported "cooking" organic aerosol (COA), but possessing different diurnal variations to what would be expected for cooking activities, contributed 18 %. Correlations between the different particle types obtained by the two aerosol mass spectrometers are also discussed. Despite wood, coal and peat being minor fuel types used for domestic space heating in urban areas, their relatively low combustion efficiencies result in a significant contribution to PM1 aerosol mass (44% and 28% of the total organic aerosol mass and non-refractory total PM1, respectively).Ambient wintertime background urban aerosol in Cork city, Ireland, was characterized using aerosol mass spectrometry. During the three-week measurement study in 2009, 93% of the ca. 1 350 000 single particles characterized by an Aerosol Time-of-Flight Mass Spectrometer (TSI ATOFMS) were classified into five organic-rich particle types, internally mixed to different proportions with elemental carbon (EC), sulphate and nitrate, while the remaining 7% was predominantly inorganic in nature. Non-refractory PM1 aerosol was characterized using a High Resolution Time-of-Flight Aerosol Mass Spectrometer (Aerodyne HR-ToF-AMS) and was also found to comprise organic aerosol as the most abundant species (62 %), followed by nitrate (15 %), sulphate (9 %) and ammonium (9 %), and chloride (5 %). Positive matrix factorization (PMF) was applied to the HR-ToF-AMS organic matrix, and a five-factor solution was found to describe the variance in the data well. Specifically, "hydrocarbon-like" organic aerosol (HOA) comprised 20% of the mass, "low-volatility" oxygenated organic aerosol (LV-OOA) comprised 18 %, "biomass burning" organic aerosol (BBOA) comprised 23 %, non-wood solid-fuel combustion "peat and coal" organic aerosol (PCOA) comprised 21 %, and finally a species type characterized by primary m/z peaks at 41 and 55, similar to previously reported "cooking" organic aerosol (COA), but possessing different diurnal variations to what would be expected for cooking activities, contributed 18 %. Correlations between the different particle types obtained by the two aerosol mass spectrometers are also discussed. Despite wood, coal and peat being minor fuel types used for domestic space heating in urban areas, their relatively low combustion efficiencies result in a significant contribution to PM1 aerosol mass (44% and 28% of the total organic aerosol mass and non-refractory total PM1, respectively).

Source apportionment of PM2.5 in Cork Harbour, Ireland using a combination of single particle mass spectrometry and quantitative semi-continuous measurements

An aerosol time-of-flight mass spectrometer (ATOFMS) was deployed for the measurement of the size resolved chemical composition of single particles at a site in Cork Harbour, Ireland for three weeks in August 2008. The ATOFMS was co-located with a suite of semi-continuous instrumentation for the measurement of particle number, elemental carbon (EC), organic carbon (OC), sulfate and particulate matter smaller than 2.5 μm in diameter (PM2.5). The temporality of the ambient ATOFMS particle classes was subsequently used in conjunction with the semi-continuous measurements to apportion PM2.5 mass using positive matrix factorisation. The synergy of the single particle classification procedure and positive matrix factorisation allowed for the identification of six factors, corresponding to vehicular traffic, marine, long-range transport, various combustion, domestic solid fuel combustion and shipping traffic with estimated contributions to the measured PM2.5 mass of 23%, 14%, 13%, 11%, 5% and 1.5% respectively. Shipping traffic was found to contribute 18% of the measured particle number (20–600 nm mobility diameter), and thus may have important implications for human health considering the size and composition of ship exhaust particles. The positive matrix factorisation procedure enabled a more refined interpretation of the single particle results by providing source contributions to PM2.5 mass, while the single particle data enabled the identification of additional factors not possible with typical semi-continuous measurements, including local shipping traffic.

Molecular composition of biogenic secondary organic aerosols using ultrahigh resolution mass spectrometry: comparing laboratory and field studies

Numerous laboratory experiments have been performed in an attempt to mimic atmospheric secondary organic aerosol (SOA) formation. However, it is still unclear how close the aerosol particles generated in laboratory experiments resemble atmospheric SOA with respect to their detailed chemical composition. In this study, we generated SOA in a simulation chamber from the ozonolysis of α-pinene and a biogenic volatile organic compound (BVOC) mixture containing α- and β-pinene, Δ3-carene, and isoprene. The detailed molecular composition of laboratory-generated SOA was compared with that of background ambient aerosol collected at a boreal forest site (Hyytiälä, Finland) and an urban location (Cork, Ireland) using direct infusion nanoelectrospray ultrahigh resolution mass spectrometry. Kendrick Mass Defect and Van Krevelen approaches were used to identify and compare compound classes and distributions of the detected species. The laboratory-generated SOA contained a distinguishable group of dimers that was not observed in the ambient samples. The presence of dimers was found to be less pronounced in the SOA from the VOC mixtures when compared to the one component precursor system. The elemental composition of the compounds identified in the monomeric region from the ozonolysis of both α-pinene and VOC mixtures represented the ambient organic composition of particles collected at the boreal forest site reasonably well, with about 70% of common molecular formulae. In contrast, large differences were found between the laboratory-generated BVOC samples and the ambient urban sample. To our knowledge this is the first direct comparison of molecular composition of laboratory-generated SOA from BVOC mixtures and ambient samples.