Analysis of <Emphasis Type="Italic">Escherichia coli</Emphasis> Isolated from Patients Affected by Crohn’s Disease

The etiopathogenesis of Crohn’s disease (CD) is still controversial: several genetic, immunologic, and environmental factors, including some bacteria, have been implicated. This study has been devised to assess the involvement of Escherichia coli in CD. Seven E. coli strains were isolated from 14 biopsies obtained from ileocolic ulcers of patients affected by inflammatory bowel disease (IBD), including six with ulcerative colitis and eight with CD. Five strains, exclusively isolated from CD patients, were found inside mucosal cells. Different PCR techniques (for chuA, yjaA, TspE4.C2, escV, and bfpB genes) were performed and PFGE was carried out to characterize these bacteria in comparison with other E. coli strains isolated from non-IBD specimens. The correlation of these characters with bacterial invasiveness on intestinal (Caco-2) and phagocytic (U937) cells was assessed. Overall our pilot data suggest that five among eight strains isolated from CD patients belonged to the adherent-invasive E. coli (AIEC) group, and were invasive on Caco-2 cells and resistant to phagocytosis. These findings suggest that these bacteria could be considered target organisms whose elimination could reduce the intestinal inflammatory process and CD progression.     

Fatty Acid Metabolism in Microorganisms

The production of pimelic acid from azelaic acid by microorganisms was studied. About 100 strains of bacteria which were able to utilize azelaic acid as a sole carbon source were isolated from soil and other natural materials. Among these bacteria, several strains produced a large quantity of an organic acid (pimelic acid) from azelaic acid in their culture fluids during the cultivation. The acid was isolated from the culture fluid of strain A133 in crystalline form. The crystal was identified as pimelic acid by physicochemical and biological methods.

From the results of investigations on the morphological and physiological characters, the bacterial strain A133 was assumed to be Micrococcus sp.     

Regulation of the glucolytic enzymes inPseudomonas putida

Summary The synthesis of glucose catabolizing enzymes is under inductive control inPseudomonas putida. Glucose, gluconate and 2-ketogluconate are the best nutritional inducers of these enzymes. Mutants unable to catabolize gluconate or 2-ketogluconate synthesized relatively high levels of glucose dehydrogenase and gluconate-6P dehydrase activities when grown in the presence of these substrates. This identifies both compounds as true inducers of these enzymes. KDGP aldolase is induced by its substrate, as evidenced by the inability of mutant cells unable to form KDGP to produce this enzyme at levels above the basal one. A 3-carbon compound appears to be the inducer of glyceraldehyde-3P dehydrogenase. This pattern of regulation suggests that there is a low degree of coordinate control in the synthesis of the glucolytic enzymes byP. putida. This is also supported by the lack of proportionality found in the levels of two enzymes governed by the same inducers, glucose dehydrogenase and gluconate-6P dehydrase, in cells grown on different conditions.Abbrevitions P phosphate - KDGP 2-Keto-3-deoxygluconate-6-phosphate - GDH glucose dehydrogenase - GNDH gluconate dehydrogenase - GK glucokinase - GNK gluconokinase - KGK ketogluconokinase - KGR 2-Ketogluconate-6-phosphate reductase - GPDH glucose-6-phosphate dehydrogenase - GNPD gluconate-6-phosphate dehydrase - KDGPA 2-Keto-3-deoxygluconate-6-phosphate aldolase - GAPDH glyceraldehyde-3-phosphate dehydrogenase     

Identification and characterization of lactic acid bacteria in ragi tape

One hundred and eighteen lactic acid bacteria (LAB) were isolated from five different types of ragi tape, a traditional dry-starter of Balinese rice wine. The isolates could be classified into three groups based on the cell shape and capability to produce gas from glucose. Group I contained 66 homofermentative cocci, group II contained seven homofermentative rods, and group III contained 45 heterofermentative rods. Among these 118 isolates, 21 isolates representing these groups were selected and were first identified using phenotypic characters. The identification performed phenotypically was confirmed by sequencing of variable region 8 (V8) of the 16S rDNA. The comparative studies led to the identification of Pediococcus pentosaceus, Enterococcus faecium, Lactobacillus curvatus, Weissella confusa, and W. paramesenteroides from the ragi tape examined.     

Plasmids in Vibrio parahemolyticus Strains Isolated in Japan and Bangladesh with Special Reference to Different Distributions

We surveyed plasmids in naturally occurring Vibrio parahemolyticus strains isolated in Japan and Bangladesh. Among the strains isolated in Japan, about half of the strains isolated from stools of patients of domestic diarrhea outbreaks as well as of travelers returning from East Asia were found to have plasmids, but no strains from foods had plasmids. In contrast, among the strains isolated in Bangladesh, none of the four strains isolated from patients had plasmids, but two out of eight strains isolated from water had plasmids, suggesting that plasmids are common in strains from the water in Bangladesh. All plasmids so far reported in V. parahemolyticus were detected in strains isolated from stools of patients. Incidences of plasmids in this organism were not so high in either area. In Japan, all plasmids were detected in strains from human intestines at 37 C, but in Bangladesh, where the temperature is around 30–40 C, the plasmids were detected in strains from the natural environment. These results suggested the possibility that these plasmids can come from different bacteria under rather high temperatures and that incidences of plasmids are influenced by the incidences of plasmids in bacteria present in the vicinity of V. parahemolyticus strains. None of these plasmids were found to have any relation to the biological characters tested.     

Evidence for the Involvement of Pathogenic Bacteria in Summer Mortalities of the Pacific Oyster <Emphasis Type="Italic">Crassostrea gigas</Emphasis>

A study was conducted to investigate the involvement of bacteria in oyster mortalities during summer. Moribund and apparently healthy oysters were sampled during mortality events along the French coast and in rearing facilities, usually when temperature reached 19°C or higher, and oysters were in the gonadal maturation phase. Hemolymph samples were aseptically withdrawn and submitted to bacteriological analysis. In healthy oysters, bacteria colonized hemolymph at low concentrations depending on the location. In most moribund oysters, bacteria were present in hemolymph and other tissues. These bacterial populations were more often diverse in oysters originating from the open sea than from facilities where animals were generally infected by a single type of bacterium. Only the dominant colonies were identified by phenotypic and genotypic characters (RFLP of GyrB gene and partial sequence of 16S rRNA gene). They belonged to a limited number of species including Vibrio aestuarianus, members of the V. splendidus group, V. natriegens, V. parahaemolyticus, and Pseudoalteromonas sp. The most frequently encountered species was V. aestuarianus (56% of isolates), which was composed of several strains closely related by their 16S rRNA gene but diverse by their phenotypic characters. They appeared intimately linked to oysters. The species within the V. splendidus group were less prevalent (25% of isolates) and more taxonomically dispersed. A majority of the dominant strains of V. aestuarianus and V. splendidus group injected to oysters induced mortality, whereas others belonging to the same species, particularly those found in mixture, appeared innocuous.     

Rhizobial Resource Associated with Epidemic Legumes in Tibet

A total of 128 bacterial test strains originated from Astragalus, Caragana, Gueldenstaedtia, Medicago, Melilotus, Oxytropis, Trifolium, and Vicia grown in Tibet were characterized phenotypically and genomically. Based upon the consensus of grouping results, they were identified as 16 putative species. Twenty-five test strains belonging to seven putative species of Agrobacterium, Bradyrhizobium, and Rhizobium might be nonsymbiotic bacteria and the remaining 103 test strains were symbiotic bacteria belonging to Mesorhizobium, Rhizobium, and Sinorhizobium meliloti. Although no novel taxon was detected in the symbiotic bacteria, several characters including the alkaliphilic psychrotolerance revealed that the Tibetan rhizobia could be ecotypes adapted to the local conditions. The results also demonstrated that frequent lateral transfer of symbiotic genes might have happened in the Tibetan rhizobia since nodC genes similar to that of S. meliloti were found in several Rhizobium test strains and all the Mesorhizobium species had very similar nodC genes despite their genomic background. All of these findings demonstrated that the Tibetan rhizobia were an important resource for further studies on rhizobial ecology and application. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The classification of luminescent bacteria

Summary The luminescent bacteria are logically placed in two genera. The common coccoid and frequently non-motile species placed byBeije-rinck first in his genusPhotobacterium, 1889 under the namePhotobacterium phosphorescens syn.Bacterium phosphorescens Fischer, should be recognized as the type species ofPhotobacterium. Other characters indicate that this genus should be placed in the FamilyPseudomonadaceae Winslowet al.. and should include other straight, rod-shaped, luminescent, polar flagellate bacteria that ferment glucose without, however, necessarily producing gas (H₂ and CO₂) as does the type species. The species that have the form of vibrios should be accepted as members of the genusVibrio as suggested by several previous investigators. They have characters much like those ofVibrio comma, the type species of the genusVibrio.     

Butterflies of the South Pacific

ABSTRACT

Larvae of the invasive mosquito Culex quinquefasciatus Say are morphologically similar to those of the native Culex pervigilans Bergroth, yet distinguishing these species can be hampered by morphological variations in Cx. quinquefasciatus. We present detail about the extent of these variations in an urban population of Cx. quinquefasciatus in Auckland. To aid in identification of this exotic species, we provide images of key diagnostic characters and some observed exceptions to these. Details regarding variation in diagnostic characters for < 3rd instar and 3rd/4th instar larvae are given. Of the nine characters used for identification, three were highly consistent (dorsal papillae, mantle plate, pecten teeth); each observed in > 90% of larvae, although these characters were not always visible. Other characters were less reliable, for instance, the expected position of seta 1a-S in relation to the pecten teeth was observed in < 10% of larvae. Further exploration of regional morphological variation in both Cx. quinquefasciatus and Cx. pervigilans is recommended, ideally with associated molecular characterisation.     

Variation and repeatability of courtship song characters among wild-caught and laboratory-rearedDrosophila montana andD. littoralis males (Diptera: Drosophilidae)

InDrosophila montana andD. littoralis (species of theD. virilis group), females use male courtship song in their mate choice in wild preferring males which produce short and dense sound pulses (Aspi and Hoikkala, 1995). In the present study these song characters were found to be repeatable among overwintered males. Male progenies of wild-caught flies reared in the laboratory, and inD. montana also the males collected in wild before overwintering, exhibited very little variation between males in these characters. Contrary to pulse characters, pulse train characters measured forD. montana song varied significantly between laboratory-reared males. Our findings suggest that inD. montana andD. littoralis song characters playing a part in sexual selection in the wild are more condition dependent than song characters which are not the direct targets of female choice.     

Cochlodinium heterolobatum n.sp.: Structure and Some Cytophysiological Aspects*

SYNOPSIS. Structure and morphogenesis, and cytochemical data on Cochlodinium heterolobatum, a new species of unarmored dinoflagellate, were derived from living and fixed material from culture. C. heterolobatum is characterized by the torsion of the girdle which descends in a left-hand spiral 1.8 turns; the sulcus having a torsion of 0.8 turn; a sulcus loop in the epicone; a tongue-shaped lobe in the right hypocone; nucleus in the epicone; and a stigma in the left epicone. Trichocysts and behavior of the nucleus during typical and atypical divisions are described in cells from cultures of different ages. A small form with the specific characters was found. Intracellular bacteria were seen and their growth followed in individuals from cultures of different ages. A possible relationship between those bacteria and the accumulation of metabolites inside old cells is discussed.     

Characterization and Phylogenetic Diversity of Carboxymethyl Cellulase Producing <Emphasis Type="Italic">Bacillus</Emphasis> Species from a Landfill Ecosystem

Total population of cellulose degrading bacteria was studied in a landfill ecosystem as a part of microbial diversity study. Samples were obtained from 3 and 5 feet depth of a local landfill being operated for past 10 years. Among many isolates, 22 bacterial strains were selected based on their capability to decompose carboxymethyl cellulose (CMC). These isolates were cultivated on agar medium with CMC as the carbon source. All isolates were Gram positive, endospore forming and alkalophilic bacteria with optimum growth pH 9–10. They were grouped based on the phenotypic and chemotaxonomic characters and representative strains of different groups along with high carboxymethyl cellulase (CMCase) producing strains were included for further characterization. Analysis of 16S rRNA gene indicated that these strains belong to different species of the genus Bacillus. Maximum CMCase activity of 4.8 U/ml at 50°C was obtained by strain LFC15. Results in the present study indicated the potential of waste land ecosystems such as landfill are potential source for isolation of industrially important microorganisms.     

Bioremediation Potential of Mercury by Bacillus Species Isolated from Marine Environment and Wastes of Steel Industry

ABSTRACT The marine environment is the most dynamic and most variable among the natural environments present on the globe due to its continuously changing patterns of salinity, sea surface temperature, pH, and pressure. Thus, bacteria inhabiting this environment possess the inbuilt mechanisms of adaptation necessary in such fluctuating environmental conditions, and the harboring of heavy metal–resistant genes adds to their efficiency with regard to metal remediation compared with their terrestrial counterparts. Two highly mercury-resistant isolates, one from the marine environment and another from steel industry waste, were identified as Bacillus thuringiensis PW-05 and Bacillus sp. SD-43, respectively, by 16S rRNA gene sequence analysis. When various characters of these two isolates, e.g., biochemical, morphological, antibiotic resistance, and tolerance to other heavy metals, were analyzed, they were found to share common features. However, the marine Bacillus isolate (PW-05) was found to be more capable than its terrestrial counterpart in terms of mercury volatilization capability, i.e., 94.72% in the case of PW-05 and 60.06% in the case of SD-43. Hence, marine bacteria can be used more efficiently than their terrestrial counterparts for enhanced bioremediation of mercury in contaminated envi-ronments.     

Anoxia can increase the rate of decay for cnidarian tissue: Using Actinia equina to understand the early fossil record

An experimental decay methodology is developed for a cnidarian model organism to serve as a comparison to the many previous such studies on bilaterians. This allows an examination of inherent bias against the fossilisation of cnidarian tissue and their diagnostic characters, under what conditions these occur, and in what way. The decay sequence of Actinia equina was examined under a series of controlled conditions. These experiments show that cnidarian decay begins with an initial rupturing of the epidermis, followed by rapid loss of recognisable internal morphological characters. This suggests that bacteria work quicker on the epidermis than autolysis does on the internal anatomy. The data also show that diploblastic tissue is not universally decayed more slowly under anoxic or reducing conditions than under oxic conditions. Indeed, some cnidarian characters decay more rapidly under anoxic conditions than they do under oxic conditions. This suggests the decay pathways acting may be different to those affecting soft bilaterian tissue such as soft epidermis and internal organs. What is most important in the decay of soft polyp anatomy is the microbial community, which can be dominated by oxic or anoxic bacteria. Different Lagerstätte, even of the same type, will inevitably have subtle difference in their bacterial communities, which among other factors, could be a control on soft polyp preservation leading to either an absence of compelling soft anthozoans (Burgess Shale) or an astonishing abundance (Qingjiang biota).     

Comparative study of two meromictic basins of Lake Banyoles (Spain) with sulphur phototrophic bacteria

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.     

Phenotypic Variations and Molecular Identification of <Emphasis Type="Italic">Salmonella enterica</Emphasis> Serovar Typhimurium Cells Under Starvation in Seawater

In seawater, enteric bacteria evolve toward a stressed state that is difficult to identify because of major alterations of their phenotype. In this study, we incubated four reference strains of S. enterica serovar Typhimurium in seawater microcosms for 10 months and studied the modifications of their main phenotypic characters. All of the strains lost some key characters used for traditional identification of the Salmonella genus. They became able to produce acetoin, and tryptophane deaminase activity became positive, but they lost the capacity to use rhamnose. We were able to show some modifications of the level of enzymatic profile as well as in their antibiotic susceptibility. The atypical cells of S. enterica serovar Typhimurium were identified by polymerase chain reaction (PCR) methods using the internal transcribed spacer region, and they were confirmed by multiplex PCR after the simultaneous amplification of the phoP, Hin, and H-li genes.     

Genotypic diversity in Oenococcus oeni by high-density microarray comparative genome hybridization and whole genome sequencing

Many bacteria display substantial intra-specific genomic diversity that produces significant phenotypic variation between strains of the same species. Understanding the genetic basis of these strain-specific phenotypes is especially important for industrial microorganisms where these characters match individual strains to specific industrial processes. Oenococcus oeni, a bacterium used during winemaking, is one such industrial species where large numbers of strains show significant differences in commercially important industrial phenotypes. To ascertain the basis of these phenotypic differences, the genomic content of ten wine strains of O. oeni were mapped by array-based comparative genome hybridization (aCGH). These strains comprised a genomically diverse group in which large sections of the reference genome were often absent from individual strains. To place the aCGH results in context, whole genome sequence was obtained for one of these strains and compared with two previously sequenced, unrelated strains. While the three strains shared a core group of conserved ORFs, up to 10% of the coding potential of any one strain was specific to that isolate. The genome of O. oeni is therefore likely to be much larger than that present in any single strain and it is these strain-specific regions that are likely to be responsible for differences in industrial phenotypes.     

A clone coding for Schizophyllum commune beta-glucosidase: homology with a yeast beta-glucosidase

Three identical clones coding for a partial sequence of the Schizophyllum commune beta-glucosidase were isolated from a cDNA library in lambda gt11, using polyclonal antibody to the enzyme. The identity was confirmed by comparison of the amino-terminus of a peptide from a protease lys-C digest with the sequence inferred from the cDNA sequence. A comparison of the sequence with that reported for a beta-glucosidase from Candida pelliculosa revealed a region in the latter with 43% identity in amino acid sequence. There was also a similarity in the S. commune beta-glucosidase to an active site sequence proposed for a S. commune endoglucanase, suggesting the possibility of a common catalytic mechanism for these two glucolytic enzymes.     

GENETIC STRUCTURE AND DIVERSITY WITHIN LOCAL POPULATIONS OF BACILLUS MYCOIDES

Sixty strains of Bacillus mycoides were isolated from each of two sites and characterized by their responses to standard metabolic tests used in bacterial taxonomy, by multilocus enzyme electrophoresis (MLEE), and by restriction-fragment-length polymorphism (RFLP) analysis of Southern blots probed with both a conserved DNA fragment derived from a Salmonella typhimurium ribosomal cistron and with two cosmid probes derived from B. mycoides ATCC strain 6463. Both MLEE and RFLP analyses indicated that the collection contained two genetically distinct sets of strains (I and II); one of these sets was further differentiated genetically by the same analyses (IIA and IIB). Standard taxonomic analysis did not distinguish these sets of strains; biochemical test profiles were similar for all isolates. The genetic distance between groups I and II is as great as that observed for recognized species of bacteria. It is proposed that these groups are sibling species having a common evolutionary descent and that their metabolic phenotype has been conserved, whereas their DNA and protein sequences have diverged. No strong evidence of geographic differentiation between strains from the two sites appeared in either genetic or phenetic characters.     

Hybridization of Cyprinus carpio and Carassius auratus,the first two exotic species in the lower Laurentian Great Lakes

Synopsis A preliminary comparison of Cyprinus carpio × Carassius auratus hybrids with the parent species is made by means of hybrid indices for 29 morphometric and 19 meristic characters. Of these 48 characters 29 were intermediate, seven were identical with one of the parents and 12 were extreme. Marked osteological differences in the crania of the parent species were noted as possible diagnostic characters for the identification of hybrids.Note