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Adherent-invasive Escherichia coli (AIEC) have been involved in Crohn’s disease (CD). Currently, AIEC are identified by time-consuming techniques based on in vitro infection of cell lines to determine their ability to adhere to and invade intestinal epithelial cells as well as to survive and replicate within macrophages. Our aim was to find signature sequences that can be used to identify the AIEC pathotype. Comparative genomics was performed between three E. coli strain pairs, each pair comprised one AIEC and one non-AIEC with identical pulsotype, sequence type and virulence gene carriage. Genetic differences were further analysed in 22 AIEC and 28 non-AIEC isolated from CD patients and controls. The strain pairs showed similar genome structures, and no gene was specific to AIEC. Three single nucleotide polymorphisms displayed different nucleotide distributions between AIEC and non-AIEC, and four correlated with increased adhesion and/or invasion indices. Here, we present a classification algorithm based on the identification of three allelic variants that can predict the AIEC phenotype with 84% accuracy. Our study corroborates the absence of an AIEC-specific genetic marker distributed across all AIEC strains. Nonetheless, point mutations putatively involved in the AIEC phenotype can be used for the molecular identification of the AIEC pathotype This work was funded by the Universitat de Girona project MPCUdG2016–009 and the Spanish Ministry of Education and Science through projects SAF2010-15896 and SAF2013-43284-P, being the last co-funded by the European Regional Development Fund. CCF was recipient of an IF grant from the Universitat de Girona (IFUDG2015/12)

The relative content of the four main bacteriochlorophyll (BChl) e homologs of several populations of brown-colored photosynthetic sulfur bacteria grown in different waterbodies have been measured by high performance liquid chromatography and statistically compared by principal component analysis. All the studied populations possessed representative pigment patterns enriched in highly alkylated bacteriochlorophyll e homologs, with average contents of 0.02±0.01%, 24.92±1.01%, 35.2±0.70%, and 39.9±0.71% for bacteriochlorophyll e1, e2, e3, and e4, respectively. These values clearly differ from those obtained for the same species growing under optimal conditions in laboratory batch cultures (4.99±1.11%, 50.34±1.73%, 28.99±0.63%, and 15.6±1.10% for bacteriochlorophyll e1, e2, e3, and e4, respectively). Multivariate statistical analyses grouped samples into two main clusters, both related to the developmental state of the population. Within these clusters, samples were arranged in several groups according to the physiological pigment response of bacterial populations to light limitation. Although bacteriochlorophyll homolog distribution cannot be considered a real taxonomic character, the data presented demonstrate that it can be useful in field studies since it reflects both the physiological status of the cells and the light regime under which the population has been growing.

Signature pigments of photosynthetic green sulfur bacteria (GSB) were found in ancient sediments collected from an abandoned clay quarry located in the Banyoles lacustrine area (Spain). The sediments belong to the Interglacial Waalian of the lower Pleistocene (0.7–1.5 millions years old) and were deposited after a marshy event occurring during that geologic period. Reverse-phase high performance liquid chromatography (RP-HPLC) analyses of acetone:methanol sediment extracts revealed that the main pigments found were carotenoids of both eukaryotic and prokaryotic photosynthetic organisms. In particular, isorenieratene (Isr) and β-isorenieratene (β-Isr) constituted the larger bacterial fraction (35–40% of the total carotenoid content), whereas okenone, a signature pigment of purple sulfur bacteria, accounted for less than 2%. Xanthophylls from oxygenic photosynthetic organisms accounted for the remaining carotenoids. Likewise, traces of degradation products of both bacteriochlorophyll (BChl) and chlorophyll (Chl) were also detected. The low concentration of Chl degradation products made proper identification of these compounds impossible. In contrast, degradation products of BChl-e such as bacteriochlorophyllide-e and bacteriopheophorbide-e were identified in the HPLC analyses, suggesting that chemical degradation of naturally occurring BChl aggregates of GSB was slower in the clay quarry sediments. The presence of signature pigments of brown-colored species of GSB (Isr, β-Isr and degradation products of BChl-e) in the sediments suggests an ancient aquatic environment where GSB were present and where episodes of sulfide-rich anoxia reaching the photic zone could be envisaged. Similarly, the large percentage of algal xanthophylls supports that algae could be an important part of the microbial photosynthetic community in this ancient ecosystem., EU. TMR Program, Contract No. FMRXCT96-0081.

(2000). Evaluation of soluble phosphate as a factor determining the density of sulfur photosynthetic bacteria in Lake Siso. SIL Proceedings, 1922-2010: Vol. 27, No. 2, pp. 850-853.

The green sulfur bacterium Chlorobium limicola UdG6040 exhibited a significant change in the spectral properties of its antenna when transferred from batch culture to a sulfide-limited chemostat. In steady-state continuous cultures, the in vivo absorption maximum of the culture changed to shorter wavelengths according to the dilution rate. The maximum difference observed was of 15 nm when cells were growing at 0.087 h–1. HPLC analyses revealed that the observed spectral change was caused by a partial enrichment of the original BChl c-containing antenna with BChl d molecules together with a change in the homolog composition of both pigments. The relative amount of BChl d reached a maximum value of 50% when cells were growing at 0.087 h–1. The content of BChl d decreased to less than the 22% when the dilution rate was diminished to 0.015 h–1. An unbalance of pigment synthesis at high dilution rates is suspected to be responsible of the changes observed in the antenna composition. Chlorosomes isolated from Chl. limicola UdG6040 growing at 0.070 h–1 contain organised pools of BChl c and BChl d in equal amounts.

The uptake of soluble phosphate by the green sulfur bacterium Chlorobium limicola UdG6040 was studied in batch culture and in continuous cultures operating at dilution rates of 0.042 or 0.064 h-1. At higher dilution rates, washout occurred at phosphate concentrations below 7.1mgr;M. This concentration was reduced to 5. 1mgr;M when lower dilution rates were used. The saturation constant for growth on phosphate (Kmgr;) was between 2.8 and 3.7mgr;M. The specific rates of phosphate uptake in continuous culture were fitted to a hyperbolic saturation model and yielded a maximum rate (Vamax) of 66 nmol P (mg protein)-1 h-1 and a saturation constant for transport (Kt) of 1.6mgr;M. In batch cultures specific rates of phosphate uptake up to 144 nmol P (mg protein)-1 h-1 were measured. This indicates a difference between the potential transport of cells and the utilization of soluble phosphate for growth, which results in a significant change in the specific phosphorus content. The phosphorus accumulated within the cells ranged from 0.4 to 1.1mgr;mol P (mg protein)-1 depending on the growth conditions and the availability of external phosphate. Transport rates of phosphate increased in response to sudden increases in soluble phosphate, even in exponentially growing cultures. This is interpreted as an advantage that enables Chl. limicola to thrive in changing environments.

Escherichia coli (E. coli), and particularly the adherent invasive E. coli (AIEC) pathotype, has been increasingly implicated in the ethiopathogenesis of Crohn’s disease (CD). E. coli strains with similar pathogenic features to AIEC have been associated with other intestinal disorders such as ulcerative colitis, colorectal cancer, and coeliac disease, but AIEC prevalence in these diseases remains largely unexplored. Since AIEC was described one decade ago, substantial progress has been made in deciphering its mechanisms of pathogenicity. However, the molecular bases that characterize the phenotypic properties of this pathotype are still not well resolved. A review of studies focused on E. coli populations in inflammatory bowel disease (IBD) is presented here and we discuss about the putative role of this species on each IBD subtype. Given the relevance of AIEC in CD pathogenesis, we present the latest research findings concerning AIEC host-microbe interactions and pathogenicity. We also review the existing data regarding the prevalence and abundance of AIEC in CD and its association with other intestinal diseases from humans and animals, in order to discuss the AIEC disease- and host-specificity. Finally, we highlight the fact that dietary components frequently found in industrialized countries may enhance AIEC colonization in the gut, which merits further investigation and the implementation of preventative measures.

Different reduced sulfur compounds (H 2 S, FeS, S 2 O 3 2− ) were tested as electron donors for dissimilatory nitrate reduction in nitrate-amended sediment slurries. Only in the free sulfide-enriched slurries was nitrate appreciably reduced to ammonia ( 0.30 μmol NH 4 + μmol NO 3 − ), with concomitant oxidation of sulfide to S 0 ( 0.55 μmol S 0 μmol S 2− ). The initial concentration of free sulfide appears as a factor determining the type of nitrate reduction. At extremely low concentrations of free S 2− (metal sulfides) nitrate was reduced via denitrification whereas at higher S 2− concentrations, dissimilatory nitrate reduction to ammonia (DNRA) and incomplete denitrification to gaseous nitrogen oxides took place. Sulfide inhibition of NO- and N 2 O- reductases is proposed as being responsible for the driving part of the electron flow from S 2− to NH 4 + .

The annual limnological dynamics of two meromictic basins of Lake Banyoles (C-III and C-IV) have been studied and compared on the basis of their physical, chemical and biological characters. Stability values calculated for both basins gave 865 g cm cm−2 and 495 g cm cm−2 for C-III and C-IV respectively. These values are in agreement with the fact that C-IV was almost completely mixed during winter. In this basin, during stratification, the monimolimnion increased in thickness as the stability increased. Isolation of the respective monimolimnia resulted in the development of anoxic conditions and the accumulation of sulphide in both C-III and C-IV, which favoured the development of dense populations of sulfur phototrophic bacteria. The purple sulphur bacterium Chromatium minus and the green sulphur bacterium Chlorobium phaeobacteroides were identified as the main components of these photosynthetic populations. The different depths at which the O2/H2S boundary was situated in both basins (and consequently the different light intensity reaching this zone) determined the growth of these bacteria. Light intensities at the chemocline of C-IV reached values up to 5% of surface incident light. In contrast, in C-III this variable was sensibly lower, with values depending on season and seldom reaching 1%. Phototrophic bacteria were consequently found earlier in C-IV than in C-III, where no significant concentrations were found until August. Finally stability is discussed as an important factor controlling chemical and biological dynamics in meromictic lakes.

The pigment composition of two species of green-colored BChl c-containing green sulfur bacteria (Chlorobium limicola and C. chlorovibrioides) and two species of brown-colored BChl e-containing ones (C. phaeobacteroides and C. phaeovibrioides) incubated at different light intensities have been studied. All species responded to the reduction of light intensity from 50 to 1 μEinstein(E) m(-2) s(-1) by an increase in the specific content of light harvesting pigments, bacteriochlorophylls and carotenoids. At critical light intensities (0.5 to 0.1 μE m(-2) s(-1)) only brown-colored chlorobia were able to grow, though at low specific rates (0.002 days(-1) mg prot(-1)). High variations in the relative content of farnesyl-bacteriochlorophyll homologues were found, in particular BChl e 1 and BChl e 4, which were tentatively identified as [M, E] and [I, E] BChlF e, respectively. The former was almost completely lost upon reduction of light intensity from 50 to 0.1 μE m(-2) s(-1), whereas the latter increased from 7.2 to 38.4% and from 13.6 to 42.0% in C. phaeobacteroides and C. phaeovibrioides, respectively. This increase in the content of highly alkylated pigment molecules inside the chlorosomes of brown species is interpreted as a physiological mechanism to improve the efficiency of energy transfer towards the reaction center. This study provides some clues for understanding the physiological basis of the adaptation of brown species to extremely low light intensities.

Denitrification rates were measured in sediments after the addition of different concentrations of FeS. A decrease of the denitrification rate was observed when high concentrations of ferrous iron (> 10 mM) were present. In the experiments with no significant concentrations of free Fe2+, the relationship between NO3− reduction and FeS concentration followed Michaelis and Menten kinetics. The maximum rate was 0.273 mmol l−1 d−1, 6 times as much as the basal rate 0.046 mmol l−1 d−1, which was attributed to organic matter; the Ks was 1.45 mM FeS. The stoichiometry of the overall reaction involving NO3− reduction and the concomitant S2− oxidation was also investigated. Measured ΔS/ΔN ratios ranged between 0.55 and 0.64, with ΣH2S + SO42− changing less than 10%. These values agree with the theoretically expected value of 0.56.

The ecological succession of two microbial planktonic populations in the chemocline of C-IV, a meromictic basin of Lake Banyoles has been studied during the stratification period of 1989 (June to October). A dense population of deep-living algae Cryptomonas phaseolus was found growing between 13 and 14 meters depth, forming peaks of 10 to 20 μg.l−1 of chlorophyll a. The physical and chemical properties of the water were continually changing during the studied period and were strongly related to the biological processes developed at the monimolimnion of C-IV. Although the monimolimnion of the basin was initially anoxic (Eh values were around +300 mV and sulphide was not present at detectable levels) soluble iron and sulphide appeared sequentially, displacing the deep-living algae population and setting the conditions for the development of a population of brown Chlorobiaceae, Chlorobium phaeobacteroides. Although Cryptomonas population abandons the chemocline (13.75 m.) and decreases its biomass, it does not disappear at all, but moves upwards (8–11 m.) leaving the zone to sulphur phototrophic bacteria which find optimal conditions to grow. The sulphide diffusion coming from sediment and the nutrient limitation were the main responsible factors accounting for the upwards migration and the decrease of growth rate of the algal population respectively.

The distribution of iron both in suspended sediment and in the water column has been studied during summer stratification in Lake Banyoles. In this lake, near bottom springs, a very fine material ‘suspended sediment’ remains in suspension. Dissolved Fe2+ in interstitial water of this suspended sediment, is related to redox potential and to the bottom water inflow. In the water column, soluble iron is present in the hypolimnion of the six different basins forming Lake Banyoles. Under those conditions Fe2+ is partially removed by sulfide produced in the anoxic sediment. In addition, a peak of Fe2+ found at the density gradient level in basins C-III, C-IV and C-VI. A three compartment model on the dynamics of the processes involving iron in Lake Banyoles is proposed. The bottom springs supply oxygen to the anoxic hypolimnion affecting chemical processes of the iron cycle. The presence of phototrophic sulfur bacteria in the anoxic monimolimnion of basins C-III and C-IV can be related to the kinetics of Fe2+ and sulfide. In C-III sulfide concentration exceeds Fe2+ concentration whereas in C-IV sulfide is not detectable and iron reached values up to 60 mM. The presence of phototrophic sulfur bacteria in iron-containing environments with no detectable sulfide is explained by the ability of such microorganisms to use FeS as electron donor instead of H2S.

The effects of inhibition of carotenoid biosynthesis by 2-hydroxybiphenyl on the photosynthetic growth, pigment composition and chlorosome structure of Chlorobium phaeobacteroides strain CL1401 were examined. At a concentration of 20 micrograms 2-hydroxybiphenyl .ml-1, carotenoid synthesis was largely inhibited (85%), but the photosynthetic growth rate was almost unaffected (mu control = 0.00525 +/- 0.00007 h-1 and mu HBP-treated = 0.00505 +/- 0.0005 h-1). Cells grown in the presence of the inhibitor were 5 microns-70 microns long, while control cells were between 2-5 microns long. Moreover, 2-hydroxybiphenyl-treated cells contained fewer, unevenly distributed chlorosomes per micron of cytoplasmic membrane with an irregular arrangement (2.5 +/- 1.5 vs of 9.1 +/- 1.9). This was concomitant to the 83% decrease in the content of bacteriochlorophyll (BChl) e in 2-hydroxybiphenyl-treated cells. Electron microscopy revealed that the shape of carotenoid-depleted chlorosomes changed from ellipsoidal to spherical, although the mean volume was similar to that of control chlorosomes. SDS-PAGE analysis of the chlorosome polypeptide composition showed that the amount of CsmA protein decreased by 60% in carotenoid-depleted chlorosomes. This was paralleled by a decrease in the baseplate BChl a content. The data suggest that carotenoids are close to the chlorosomal baseplate, where they carry out both structural and photoprotective functions.

Among photosynthetic microorganisms, Green Sulfur Bacteria are unique due to their capacity to grow at very low light intensities. Their antenna complexes, the chlorosomes, contain the bacteriochlorophylls (BChl c, d or e) the carotenoids (Car), and BChl a in the baseplate [1]. The high packaging and arrangement of pigments within the chlorosomes convert them in highly efficient light-harvesting structures. Brown coloured species can grow under extremely low light conditions both by increasing their specific content of antenna pigments and by modifying their BChl e homolog composition [2]. In contrast, such adaptations were found to be less apparent in green coloured species.

Green species of Chlorobiaceae contain either BChl c or d as main antenna pigments, though in some cases may coexist [1-3]. Inside the chlorosomes, BChl molecules exist as a series of aggregated homologs arranged as rod elements [3]. Chlorosome bacteriochlorophylls capture light energy, which is sequentially transferred to the RC through distinct excitation carriers: the BChl a chlorosome baseplate, FMO proteins, and the membrane bound BChl a-protein complexes [4].

Green sulfur bacteria are unique within photosynthetic microorganisms in their capacity to grow at extremely low light intensities. This ability is mainly related with the structure of their photosynthetic antenna, the chlorosomes, oblong bodies attached to the cytoplasmic membrane and tightly packed with antenna pigments. All green bacteria contain bacteriochlorophyll (BChl) c, d or e, in a mixture of several homologs. Together with antenna BChls, chlorosomes contain variable amounts of carotenoids and a BChl a baseplate, which acts as an intermediate in energy transfer [1].

A reversed-phase High Performance Liquid Cromatography (HPLC) method has been developed to accurately separate bacteriochlorophyllsc, d ande homologues in a reasonably short run time of 60 minutes. By using this method, two well-defined groups of bacteriochlorophyll homologue peaks can be discriminated. The first one consists of 4 peaks (min 24 to 30), which corresponds to the four main farnesyl homologues. The second peak subset is formed by a cluster of up to 10 minor peaks (min 33 to 40). These peaks can be related with series of several alcohol esters of the different chlorosome chlorophylls. The number of homologues was, however, quite variable depending on both, the bacteriochlorophyll and the bacterial species. The method hereby described, also provides a good separation of other photosynthetic pigments, either bacterial (Bacteriochlorophylla, chlorobactene, isorenieratene and okenone) or algal ones (Chlorophylla, Pheophytina and β-carotene). A preliminary screening of the homologue composition of several green photosynthetic bacterial species and isolates, has revealed different relative quantitative patterns. These differences seem to be related to physiological aspects rather than to taxonomic ones. The application of the method to the study of natural populations avoids the typical drawbacks on the pigment identification of overlapping eukaryotic and prokaryotic phototrophic microorganisms, giving further information about their physiological status.

The microbial ecology of the filamentous phototrophic bacterium, Chloronema giganteum, has been studied in the water column of three central European lakes (Schiein, Buchen and Vechten). In these lakes an anoxic layer, termed the transition zone, was located between the oxycline and the redoxcline. The migration capacity of Chloronema through this zone appears to be responsible for the natural preponderance of either straight or spiral forms. When the transition zone is less than 1 m thick the straight form is dominant, but when this transition zone is wider than 2 m the spiral form is enriched. The intermediate situations favour both filamentous forms.

The annual dynamics of the phototrophic bacterial populations developing in the anoxic layers has been monitored in three basins of the northern area of Lake Banyoles (Spain). Although two of the studied basins are meromictic and one is holomictic, chemical properties of the water are almost identical. Therefore, differences in both the spatial and temporal distribution, as well as in the composition of phototrophic bacterial communities, dominated by Chlorobium phaeobacteroides and Chromatium minus, are discussed on the basis of the structural and morphometric characteristics of each basin. Both species showed the same physiological adaptations to light intensity changes by modifying the carotenoid/bacteriochlorophyll ratio. Light reaching the oxic-anoxic boundary appears to be the most important factor controlling the growth of phototrophic bacteria in Lake Banyoles. The oxic-anoxic boundary becomes shallower as summer advances, until enough light is available for bacterial photosynthesis.