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Sample records for rhizobium bacteroid development

  1. Carbon Metabolism Enzymes of Rhizobium tropici Cultures and Bacteroids.

    PubMed

    Romanov, V I; Hernández-Lucas, I; Martínez-Romero, E

    1994-07-01

    We determined the activities of selected enzymes involved in carbon metabolism in free-living cells of Rhizobium tropici CFN299 grown in minimal medium with different carbon sources and in bacteroids of the same strain. The set of enzymatic activities in sucrose-grown cells suggests that the pentose phosphate pathway, with the participation of the Entner-Doudoroff pathway, is probably the primary route for sugar catabolism. In glutamate- and malate-grown cells, high activities of the gluconeogenic enzymes (phosphoenolpyruvate carboxykinase, fructose-6-phosphate aldolase, and fructose bisphosphatase) were detected. In bacteroids, isolated in Percoll gradients, the levels of activity for many of the enzymes measured were similar to those of malate-grown cells, except that higher activities of glucokinase, glucose-6-phosphate dehydrogenase, and NAD-dependent phosphogluconate dehydrogenase were detected. Phosphoglucomutase and UDP glucose pyrophosphorylase showed high and constant levels under all growth conditions and in bacteroids. PMID:16349319

  2. Fluorescence studies with malate dehydrogenase from rhizobium japonicum 3I1B-143 bacteroids: a two-tryptophan containing protein

    NASA Astrophysics Data System (ADS)

    Ghiron, Camillo A.; Eftink, Maurice R.; Waters, James K.; Emerich, David W.

    1990-05-01

    A number of fluorescence studies, both of trp residues and bound NADH, have been reported for porcine MDH. The large number of trp residues (6) complicates the interpretation of some studies. To circumvent this we have performed studies with a two tryptophan (per subunit) MDH from Rhizobium japonicum 311B-143 bacteroids. We have performed phase/modulation fluorescence lifetime measurements, as a function of temperature and added quencher KI, in order to resolved the 1.3 ns (blue) and 6.6 ns (red) contributions from the two classes of trp residues. Anisotropy decay studies have also been performed. The binding of NADH dynamically quenches the fluorescence of both tip residues, but, unlike mammalian cytoplasmic and mitochondrial MDH, there is not a large enhancement in fluorescence of bound NADH upon forming a ternary complex with either tartronic acid or D-malonate.

  3. Membrane energization in relation with nitrogen fixation in Azotobacter vinelandii and Rhizobium leguminosarum bacteroids.

    PubMed

    Veeger, C; Laane, C; Scherings, G; van Zeeland Wolbers, L

    1978-01-01

    Nitrogen fixation in A. vinelandii and R. leguminosarum bacteroides shows identical characteristics with respect to the dependence on membrane energization, the sensitivity to uncouplers, the ATP/ADP-ratio, and the dependences on flavodoxinhydroquinone as electrondonor. Although we have been successful in preparing inside-out vesicles which can be energized, attempts to couple these membranes to N2-ase were still unsuccessful. One of the major problems could be the failure to energize these vesicles directly by ATP. Although subject to polymerisation after addition of MgCl2, it could be shown that the actual mol.wt. of the O2-stable N2-ase complex is about 300,000 in agreement with a 1:1:1 stoichiometry of the three constituent proteins, namely, component I, component II and the 2Fe-2S protein. PMID:667180

  4. Terminal bacteroid differentiation in the legume-rhizobium symbiosis: nodule-specific cysteine-rich peptides and beyond.

    PubMed

    Alunni, Benoît; Gourion, Benjamin

    2016-07-01

    Contents 411 I. 411 II. 412 III. 412 IV. 413 V. 414 VI. 414 VII. 415 VIII. 415 416 References 416 SUMMARY: Terminal bacteroid differentiation (TBD) is a remarkable case of bacterial cell differentiation that occurs after rhizobia are released intracellularly within plant cells of symbiotic legume organs called nodules. The hallmarks of TBD are cell enlargement, genome amplification and membrane permeabilization. This plant-driven process is governed by a large family of bacteroid-targeted nodule-specific cysteine-rich (NCR) peptides that were until recently thought to be restricted to a specific lineage of the legume family, including the model plant Medicago truncatula. Recently, new plant and bacterial factors involved in TBD have been identified, challenging our view of this phenomenon at mechanistic and evolutionary levels. Here, we review the recent literature and discuss emerging questions about the mechanisms and the role(s) of TBD. PMID:27241115

  5. Development of new host-specific Bacteroides qPCRs for the identification of fecal contamination sources in water.

    PubMed

    Gómez-Doñate, Marta; Casanovas-Massana, Arnau; Muniesa, Maite; Blanch, Anicet R

    2016-02-01

    Bacteroides spp. have been proposed as indicators of fecal contamination in microbial source tracking (MST) methodologies. The aim of this study was to develop new qPCR assays that target host-specific Bacteroidal 16S ribosomal RNA genes, to determine the source of fecal contamination in water. Denaturing gradient gel electrophoresis (DGGE) was used to select for host-specific bands of Bacteroides associated with a fecal pollution source and later to design four qPCR host-specific assays. A set of common primers for Bacteroides spp., four different Bacteroides spp. host-associated hydrolysis probes (human, cattle, pig, and poultry), and one hydrolysis probe for the Bacteroides genus were designed. This set of qPCR assays together with other previously developed Bacteroidetes MST targets were used to analyze water samples with fecal contamination from the four sources studied. The host-specific Bacteroides qPCRs designed for human (HMprobeBac), pig (PGprobeBac), and poultry (PLprobeBac) were highly specific for its sources (1.0, 0.97, and 1.0, respectively) although its sensitivity was lower (0.45, 0.50, and 0.73, respectively). The cattle-specific qPCR was totally unspecific and was discarded for future experiments. When compared to previously designed assays, the human and pig qPCRs showed better accuracies (0.86 and 0.84) than their counterparts HF183 and Pig-2-Bac (0.38 and 0.65). Thus, the newly designed human, pig, and poultry qPCR assays outperform other methods developed until date and may be useful for source tracking purposes. PMID:26763626

  6. Microgravity effects on the legume/Rhizobium symbiosis

    NASA Astrophysics Data System (ADS)

    Urban, James E.

    1997-01-01

    Symbiotic nitrogen fixation is of critical importance to world agriculture and likely will be a critical part of life support systems developed for prolonged missions in space. Bacteroid formation, an essential step in an effective Dutch White Clover/Rhizobium leguminosarum bv trifolii symbiosis, is induced by succinic acid which is produced by the plant and which is bound and incorporated by the bacterium. Aspirin mimics succinate in its role as a bacteroid inducer and measures of aspirin binding mimiced measurements of succinate binding. In normal gravity (1×g), rhizobium bacteria immediately bound relatively high levels of aspirin (or succinate) in a readily reversible manner. Within a few seconds a portion of this initially bound aspirin became irreversibly bound. In the microgravity environment aboard the NASA 930 aircraft, rhizobia did not display the initial reversible binding of succinate, but did display a similar kinetic pattern of irreversible binding, and ultimately bound 32% more succinate (Acta Astronautica 36:129-133, 1995.) In normal gravity succinate treated cells stop dividing and swell to their maximum size (twice the normal cell volume) within a time equivalent to the time required for two normal cell doublings. Swelling in microgravity was tested in FPA and BPM sample holders aboard the space shuttle (USML-1, and STS-54, 57, and 60.) The behavior of cells in the two sample holders was similar, and swelling behavior of cells in microgravity was identical to behavior in normal gravity.

  7. [The defense and regulatory mechanisms during development of legume-Rhizobium symbiosis].

    PubMed

    Glian'ko, A K; Akimova, G P; Sokolova, M G; Makarova, L E; Vasil'eva, G G

    2007-01-01

    The roles of indolylacetic acid, the peroxidase system, catalase, active oxygen species, and phenolic compounds in the physiological and biochemical mechanisms involved in the autoregulation of nodulation in the developing legume-Rhizobium symbiosis were studied. It was inferred that the concentration of indolylacetic acid in the roots of inoculated plants, controlled by the enzymes of the peroxidase complex, is the signal permitting or limiting nodulation at the initial stages of symbiotic interaction. Presumably, the change in the level of active oxygen species is determined by an antioxidant activity of phenolic compounds. During the development of symbiosis, phytohormones, antioxidant enzymes, and active oxygen species may be involved in the regulation of infection via both a direct antibacterial action and regulation of functional activity of the host plant defense systems. PMID:17619575

  8. Rhizobium lipopolysaccharide modulates infection thread development in white clover root hairs.

    PubMed Central

    Dazzo, F B; Truchet, G L; Hollingsworth, R I; Hrabak, E M; Pankratz, H S; Philip-Hollingsworth, S; Salzwedel, J L; Chapman, K; Appenzeller, L; Squartini, A

    1991-01-01

    The interaction between Rhizobium lipopolysaccharide (LPS) and white clover roots was examined. The Limulus lysate assay indicated that Rhizobium leguminosarum bv. trifolii (hereafter called R. trifolii) released LPS into the external root environment of slide cultures. Immunofluorescence and immunoelectron microscopy showed that purified LPS from R. trifolii 0403 bound rapidly to root hair tips and infiltrated across the root hair wall. Infection thread formation in root hairs was promoted by preinoculation treatment of roots with R. trifolii LPS at a low dose (up to 5 micrograms per plant) but inhibited at a higher dose. This biological activity of LPS was restricted to the region of the root present at the time of exposure to LPS, higher with LPS from cells in the early stationary phase than in the mid-exponential phase, incubation time dependent, incapable of reversing inhibition of infection by NO3- or NH4+, and conserved among serologically distinct LPSs from several wild-type R. trifolii strains (0403, 2S-2, and ANU843). In contrast, infections were not increased by preinoculation treatment of roots with LPSs from R. leguminosarum bv. viciae strain 300, R. meliloti 102F28, or members of the family Enterobacteriaceae. Most infection threads developed successfully in root hairs pretreated with R. trifolii LPS, whereas many infections aborted near their origins and accumulated brown deposits if pretreated with LPS from R. meliloti 102F28. LPS from R. leguminosarum 300 also caused most infection threads to abort. Other specific responses of root hairs to infection-stimulating LPS from R. trifolii included acceleration of cytoplasmic streaming and production of novel proteins. Combined gas chromatography-mass spectroscopy and proton nuclear magnetic resonance analyses indicated that biologically active LPS from R. trifolii 0403 in the early stationary phase had less fucose but more 2-O-methylfucose, quinovosamine, 3,6-dideoxy-3-(methylamino)galactose, and

  9. Rhizobium meliloti mutants unable to synthesize anthranilate display a novel symbiotic phenotype.

    PubMed Central

    Barsomian, G D; Urzainqui, A; Lohman, K; Walker, G C

    1992-01-01

    Analyses of Rhizobium meliloti trp auxotrophs suggest that anthranilate biosynthesis by the R. meliloti trpE(G) gene product is necessary during nodule development for establishment of an effective symbiosis. trpE(G) mutants, as well as mutants blocked earlier along this pathway in aromatic amino acid biosynthesis, form nodules on alfalfa that have novel defects. In contrast, R. meliloti trp mutants blocked later in the tryptophan-biosynthetic pathway form normal, pink, nitrogen-fixing nodules. trpE(G) mutants form two types of elongated, defective nodules containing unusually extended invasion zones on alfalfa. One type contains bacteroids in its base and is capable of nitrogen fixation, while the other lacks bacteroids and cannot fix nitrogen. The trpE(G) gene is expressed in normal nodules. Models are discussed to account for these observations, including one in which anthranilate is postulated to act as an in planta siderophore. Images PMID:1320610

  10. Alfalfa Enod12 genes are differentially regulated during nodule development by Nod factors and Rhizobium invasion.

    PubMed Central

    Bauer, P; Crespi, M D; Szécsi, J; Allison, L A; Schultze, M; Ratet, P; Kondorosi, E; Kondorosi, A

    1994-01-01

    MsEnod12A and MsEnod12B are two early nodulin genes from alfalfa (Medicago sativa). Differential expression of these genes was demonstrated using a reverse transcription-polymerase chain reaction approach. MsEnod12A RNA was detected only in nodules and not in other plant tissues. In contrast, MsEnod12B transcripts were found in nodules and also at low levels in roots, flowers, stems, and leaves. MsEnod12B expression was enhanced in the root early after inoculation with the microsymbiont Rhizobium meliloti and after treatment with purified Nod factors, whereas MsEnod12A induction was detected only when developing nodules were visible. In situ hybridization showed that in nodules, MsEnod12 expression occurred in the infection zone. In empty Fix- nodules the MsEnod12A transcript level was much reduced, and in spontaneous nodules it was not detectable. These data indicate that MsEnod12B expression in roots is related to the action of Nod factors, whereas MsEnod12A expression is associated with the invasion process in nodules. Therefore, alfalfa possesses different mechanisms regulating MsEnod12A and MsEnod12B expression. PMID:8066132

  11. Characterization of the lipopolysaccharide from a Rhizobium phaseoli mutant that is defective in infection thread development.

    PubMed Central

    Carlson, R W; Kalembasa, S; Turowski, D; Pachori, P; Noel, K D

    1987-01-01

    The lipopolysaccharide (LPS) from a Rhizobium phaseoli mutant, CE109, was isolated and compared with that of its wild-type parent, CE3. A previous report has shown that the mutant is defective in infection thread development, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis shows that it has an altered LPS (K. D. Noel, K. A. VandenBosch, and B. Kulpaca, J. Bacteriol. 168:1392-1462, 1986). Mild acid hydrolysis of the CE3 LPS released a polysaccharide and an oligosaccharide, PS1 and PS2, respectively. Mild acid hydrolysis of CE109 LPS released only an oligosaccharide. Chemical and immunochemical analyses showed that CE3-PS1 is the antigenic O chain of this strain and that CE109 LPS does not contain any of the major sugar components of CE3-PS1. CE109 oligosaccharide was identical in composition to CE3-PS2. The lipid A's from both strains were very similar in composition, with only minor quantitative variations. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of CE3 and CE109 LPSs showed that CE3 LPS separated into two bands, LPS I and LPS II, while CE109 had two bands which migrated to positions similar to that of LPS II. Immunoblotting with anti-CE3 antiserum showed that LPS I contains the antigenic O chain of CE3, PS1. Anti-CE109 antiserum interacted strongly with both CE109 LPS bands and CE3 LPS II and interacted weakly with CE3 LPS I. Mild-acid hydrolysis of CE3 LPS I, extracted from the polyacrylamide gel, showed that it contained both PS1 and PS2. The results in this report showed that CE109 LPS consists of only the lipid A core and is missing the antigenic O chain. Images PMID:3667520

  12. Evaluation of nitrate reductase activity in Rhizobium japonicum

    SciTech Connect

    Streeter, J.G.; DeVine, P.J.

    1983-08-01

    Nitrate reductase activity was evaluated by four approaches, using four strains of Rhizobium japonicum and 11 chlorate-resistant mutants of the four strains. It was concluded that in vitro assays with bacteria or bacteroids provide the most simple and reliable assessment of the presence or absence of nitrate reductase. Nitrite reductase activity with methyl viologen and dithionite was found, but the enzyme activity does not confound the assay of nitrate reductase. 18 references

  13. A Peptidoglycan-Remodeling Enzyme Is Critical for Bacteroid Differentiation in Bradyrhizobium spp. During Legume Symbiosis.

    PubMed

    Gully, Djamel; Gargani, Daniel; Bonaldi, Katia; Grangeteau, Cédric; Chaintreuil, Clémence; Fardoux, Joël; Nguyen, Phuong; Marchetti, Roberta; Nouwen, Nico; Molinaro, Antonio; Mergaert, Peter; Giraud, Eric

    2016-06-01

    In response to the presence of compatible rhizobium bacteria, legumes form symbiotic organs called nodules on their roots. These nodules house nitrogen-fixing bacteroids that are a differentiated form of the rhizobium bacteria. In some legumes, the bacteroid differentiation comprises a dramatic cell enlargement, polyploidization, and other morphological changes. Here, we demonstrate that a peptidoglycan-modifying enzyme in Bradyrhizobium strains, a DD-carboxypeptidase that contains a peptidoglycan-binding SPOR domain, is essential for normal bacteroid differentiation in Aeschynomene species. The corresponding mutants formed bacteroids that are malformed and hypertrophied. However, in soybean, a plant that does not induce morphological differentiation of its symbiont, the mutation does not affect the bacteroids. Remarkably, the mutation also leads to necrosis in a large fraction of the Aeschynomene nodules, indicating that a normally formed peptidoglycan layer is essential for avoiding the induction of plant immune responses by the invading bacteria. In addition to exopolysaccharides, capsular polysaccharides, and lipopolysaccharides, whose role during symbiosis is well defined, our work demonstrates an essential role in symbiosis for yet another rhizobial envelope component, the peptidoglycan layer. PMID:26959836

  14. Isolation of Bacteroides from fish and human fecal samples for identification of unique molecular markers.

    PubMed

    Kabiri, Leila; Alum, Absar; Rock, Channah; McLain, Jean E; Abbaszadegan, Morteza

    2013-12-01

    Bacteroides molecular markers have been used to identify human fecal contamination in natural waters, but recent work in our laboratory confirmed cross-amplification of several human-specific Bacteroides spp. assays with fecal DNA from fish. For identification of unique molecular markers, Bacteroides from human (n = 4) and fish (n = 7) fecal samples were cultured and their identities were further confirmed using Rapid ID 32A API strips. The 16S rDNA from multiple isolates from each sample was PCR amplified, cloned, and sequenced to identify unique markers for development of more stringent human-specific assays. In human feces, Bacteroides vulgatus was the dominant species (75% of isolates), whereas in tilapia feces, Bacteroides eggerthii was dominant (66%). Bacteroides from grass carp, channel catfish, and blue catfish may include Bacteroides uniformis, Bacteroides ovatus, or Bacteroides stercoris. Phylogenic analyses of the 16S rRNA gene sequences showed distinct Bacteroides groupings from each fish species, while human sequences clustered with known B. vulgatus. None of the fish isolates showed significant similarity to Bacteroides sequences currently deposited in NCBI (National Center for Biotechnology Information). This study expands the current sequence database of cultured fish Bacteroides. Such data are essential for identification of unique molecular markers in human Bacteroides that can be utilized in differentiating fish and human fecal contamination in water samples. PMID:24313449

  15. Development of a Gene Inactivation System for Bacteroides forsythus: Construction and Characterization of a BspA Mutant

    PubMed Central

    Honma, Kiyonobu; Kuramitsu, Howard K.; Genco, Robert J.; Sharma, Ashu

    2001-01-01

    Bacteroides forsythus is a gram-negative anaerobic bacterium associated with periodontitis. The bspA gene encoding a cell surface associated leucine-rich repeat protein (BspA) involved in adhesion to fibronectin and fibrinogen was recently cloned from this bacterium in our laboratory. We now describe the construction of a BspA-defective mutant of B. forsythus. This is the first report describing the generation of a specific gene knockout mutant of B. forsythus, and this procedure should be useful in establishing the identity of virulence-associated factors in these organisms. PMID:11402017

  16. Comparison of nucleic acid content in populations of free-living and symbiotic Rhizobium meliloti by flow microfluorometry.

    PubMed Central

    Paau, A S; Lee, D; Cowles, J R

    1977-01-01

    Populations of symbiotic Rhizobium meliloti extracted from alfalfa nodules were shown by flow microfluorometry to contain a significant number of bacteroids with higher nucleic acid content than the free-living rhizobia. Bacteroids with lower nucleic acid content than the free-living bacteria were not detected in significant quantities in these populations. These results indicate that the incapability of bacteroids to reestablish growth in nutrient media may not be caused by a decrease in nucleic acid content of the symbiotic rhizobia. PMID:838682

  17. Effects of microgravity on the binding of acetylsalicylic acid by Rhizobium leguminosarum bv. trifolii

    NASA Astrophysics Data System (ADS)

    Urban, James E.; Gerren, Richard; Zoelle, Jeffery

    1995-07-01

    Bacteroids can be induced in vitro by treating growing Rhizobium leguminosarum bv. trifolii with succinic acid or succinic acid structural analogs like acetylsalicylic acid. Quantitating bacteroid induction by measuring acetylsalicylic binding under normal (1 g) conditions showed two forms of binding to occur. In one form of binding cells immediately bound comparatively high levels of acetylsalicylic acid, but the binding was quickly reversed. The second form of binding increased with time by first-order kinetics, and reached saturation in 40 s. Similar experiments performed in the microgravity environment aboard the NASA 930 aircraft showed only one form of binding and total acetylsalicylic acid bound was 32% higher than at 1 g.

  18. (A structural assessment of the role of the cell surface carbohydrates of Rhizobium in the Rhizobium/legume symbiosis)

    SciTech Connect

    Hollingsworth, R.I.

    1991-01-01

    Research continued on the study of cell surface carbohydrates of Rhizobium. Objectives include: To characterize, at a structural level, the differences between the lipopolysaccharides of a representative number of strains from different Rhizobium species to determine which features of LPS structure are species-specific and might, therefore, be determinants of host specificity. Determine the effect(s) of nod gene induction on the structure of Rhizobium lipopolysaccharides and determine whether synthesis of a modified LPS molecule or a new surface glycoconjugate is initiated by nod gene induction. Develop a non-chemical means for rapidly screening large numbers of bacterial strains in order to determine which glycoconjugate structural features are conserved between strains of the same species. Provide the necessary structural information which, when coupled with developments in the rapidly expanding field of Rhizobium genetics, should lead to a clear understanding of the role of Rhizobium surface glycoconjugates in host/symbiont interactions. Progress is discussed.

  19. A rhizobium leguminosarum mutant defective in symbiotic iron acquisition

    SciTech Connect

    Nadler, K.D.; Chen, Jing-Wen; John, T.R. ); Johnston, A.W.B. )

    1990-02-01

    Iron acquisition by symbiotic Rhizobium spp. is essential for nitrogen fixation in the legume root nodule symbiosis. Rhizobium leguminosarum 116, an ineffective mutant strain with a defect in iron acquisition, was isolated after nitrosoguanidine mutagenesis of the effective strain 1062. The pop-1 mutation in strain 116 imparted to it a complex phenotype, characteristic of iron deficiency. Several iron(III)-solubilizing agents, such as citrate, hydroxyquinoline, and dihydroxybenzoate, stimulated growth of 116 on low-iron solid medium; anthranilic acid, the R. leguminosarum siderophore, inhibited low-iron growth of 116. The initial rate of {sup 55}Fe uptake by suspensions of iron-starved 116 cells was 10-fold less than that of iron-starved wild-type cells. Electron microscopic observations revealed no morphological abnormalities in the small, white nodules induced by 116. Nodule cortical cells were filled with vesicles containing apparently normal bacteroids. No premature degeneration of bacteroids or of plant cell organelles was evident. The authors mapped pop-1 by R plasmid-mediated conjugation and recombination to the ade-27-rib-2 region of the R. leguminosarum chromosome. No segregation of pop-1 and the symbiotic defect was observed among the recombinants from these crosses. Cosmid pKN1, a pLAFR1 derivative containing a 24-kilobase-pair fragment of R. leguminosarum DNA, conferred on 116 the ability to grow on dipyridyl medium and to fix nitrogen symbiotically.

  20. CERBERUS, a novel U-box protein containing WD-40 repeats, is required for formation of the infection thread and nodule development in the legume-Rhizobium symbiosis.

    PubMed

    Yano, Koji; Shibata, Satoshi; Chen, Wen-Li; Sato, Shusei; Kaneko, Takakazu; Jurkiewicz, Anna; Sandal, Niels; Banba, Mari; Imaizumi-Anraku, Haruko; Kojima, Tomoko; Ohtomo, Ryo; Szczyglowski, Krzysztof; Stougaard, Jens; Tabata, Satoshi; Hayashi, Makoto; Kouchi, Hiroshi; Umehara, Yosuke

    2009-10-01

    Endosymbiotic infection of legume plants by Rhizobium bacteria is initiated through infection threads (ITs) which are initiated within and penetrate from root hairs and deliver the endosymbionts into nodule cells. Despite recent progress in understanding the mutual recognition and early symbiotic signaling cascades in host legumes, the molecular mechanisms underlying bacterial infection processes and successive nodule organogenesis are still poorly understood. We isolated a novel symbiotic mutant of Lotus japonicus, cerberus, which shows defects in IT formation and nodule organogenesis. Map-based cloning of the causal gene allowed us to identify the CERBERUS gene, which encodes a novel protein containing a U-box domain and WD-40 repeats. CERBERUS expression was detected in the roots and nodules, and was enhanced after inoculation of Mesorhizobium loti. Strong expression was detected in developing nodule primordia and the infected zone of mature nodules. In cerberus mutants, Rhizobium colonized curled root hair tips, but hardly penetrated into root hair cells. The occasional ITs that were formed inside the root hair cells were mostly arrested within the epidermal cell layer. Nodule organogenesis was aborted prematurely, resulting in the formation of a large number of small bumps which contained no endosymbiotic bacteria. These phenotypic and genetic analyses, together with comparisons with other legume mutants with defects in IT formation, indicate that CERBERUS plays a critical role in the very early steps of IT formation as well as in growth and differentiation of nodules. PMID:19508425

  1. Characterization of bacteroides melaninogenicus.

    PubMed Central

    Harding, G K; Sutter, V L; Finegold, S M; Bricknell, K S

    1976-01-01

    Fifty-eight human isolates of Bacteroides melaninogenicus, 42 from a variety of clinical infections and the rest from normal flora, were studied for pigment production and ultraviolet light fluorescence and by forty biochemical and other tests, including end-product analysis by gas-liquid chromatography. In a number of instances, tests were repeated several times and the results were reproducible. Agar plate dilution susceptibility tests were also performed to 12 antimicrobial agents. These 58 strains could be reliably placed into three groups, corresponding to the three subspecies described, based on seven characteristics. These included acid production in peptone-yeast-glucose medium, production of n-butyric acid from peptone-yeast-glucose medium, esculin hydrolysis, starch hydrolysis, indole production, effect on milk, and lipase production. Production of hydrogen gas in peptone-yeast-fructose medium may be another distinguishing characteristic. In general there was not much difference in the susceptibility of the three groups to the various antimicrobial agents tested. Two strains had a minimal inhibitory concentration of penicillin G of 16 and 32 U/ml, respectively. Three strains did not produce a black pigment in spite of prolonged incubation on blood-containing media. PMID:10317

  2. Modulation of development, growth dynamics, wall crystallinity, and infection sites in white clover root hairs by membrane chitolipooligosaccharides from Rhizobium leguminosarum biovar trifolii.

    PubMed Central

    Dazzo, F B; Orgambide, G G; Philip-Hollingsworth, S; Hollingsworth, R I; Ninke, K O; Salzwedel, J L

    1996-01-01

    We used bright-field, time-lapse video, cross-polarized, phase-contrast, and fluorescence microscopies to examine the influence of isolated chitolipooligosaccharides (CLOSs) from wild-type Rhizobium leguminosarum bv. trifolii on development of white clover root hairs, and the role of these bioactive glycolipids in primary host infection. CLOS action caused a threefold increase in the differentiation of root epidermal cells into root hairs. At maturity, root hairs were significantly longer because of an extended period of active elongation without a change in the elongation rate itself. Time-series image analysis showed that the morphological basis of CLOS-induced root hair deformation is a redirection of tip growth displaced from the medial axis as previously predicted. Further studies showed several newly described infection-related root hair responses to CLOSs, including the localized disruption of the normal crystallinity in cell wall architecture and the induction of new infection sites. The application of CLOS also enabled a NodC- mutant of R. leguminosarum bv. trifolii to progress further in the infection process by inducing bright refractile spot modifications of the deformed root hair walls. However, CLOSs did not rescue the ability of the NodC- mutant to induce marked curlings or infection threads within root hairs. These results indicate that CLOS Nod factors elicit several host responses that modulate the growth dynamics and symbiont infectibility of white clover root hairs but that CLOSs alone are not sufficient to permit successful entry of the bacteria into root hairs during primary host infection in the Rhizobium-clover symbiosis. PMID:8655563

  3. Fecal detection of enterotoxigenic Bacteroides fragilis.

    PubMed

    Chen, L A; Van Meerbeke, S; Albesiano, E; Goodwin, A; Wu, S; Yu, H; Carroll, K; Sears, C

    2015-09-01

    Bacteroides fragilis is a common colonic symbiote of which one subtype, enterotoxigenic Bacteroides fragilis (ETBF), causes inflammatory diarrhea. However, asymptomatic ETBF colonization is common. Through its primary virulence factor, B. fragilis toxin (BFT), ETBF causes asymptomatic, chronic colitis in C57BL/6 mice and increased colon tumorigenesis in multiple intestinal neoplasia mice. Human studies suggest an association between ETBF infection, inflammatory bowel disease, and colon cancer. Additional studies on ETBF epidemiology are, therefore, crucial. The goal of this study is to develop a reliable fecal diagnostic for ETBF. To develop a sensitive assay for ETBF, we tested multiple protocols on mouse stools spiked with serially diluted ETBF. Each assay was based on either touchdown or quantitative polymerase chain reaction (qPCR) and used primers targeted to bft to detect ETBF. Using touchdown PCR or qPCR, the mean ETBF detection limit was 1.55 × 10(6) colony-forming units (CFU)/g stool and 1.33 × 10(4) CFU/g stool, respectively. Augmentation of Bacteroides spp. growth in fecal samples using PYGB (Peptone Yeast Glucose with Bile) broth enhanced ETBF detection to 2.93 × 10(2) CFU/g stool using the touchdown PCR method and 2.63 × 10(2) CFU/g stool using the qPCR method. Fecal testing using combined culture-based amplification and bft touchdown PCR is a sensitive assay for the detection of ETBF colonization and should be useful in studying the role of ETBF colonization in intestinal diseases, such as inflammatory bowel disease and colon cancer. We conclude that touchdown PCR with culture-based amplification may be the optimal ETBF detection strategy, as it performs as well as qPCR with culture-based amplification, but is a less expensive technique. PMID:26173688

  4. [A structural assessment of the role of the cell surface carbohydrates of Rhizobium in the Rhizobium/legume symbiosis]. Progress report, June 1989--June 1991

    SciTech Connect

    Hollingsworth, R.I.

    1991-12-31

    Research continued on the study of cell surface carbohydrates of Rhizobium. Objectives include: To characterize, at a structural level, the differences between the lipopolysaccharides of a representative number of strains from different Rhizobium species to determine which features of LPS structure are species-specific and might, therefore, be determinants of host specificity. Determine the effect(s) of nod gene induction on the structure of Rhizobium lipopolysaccharides and determine whether synthesis of a modified LPS molecule or a new surface glycoconjugate is initiated by nod gene induction. Develop a non-chemical means for rapidly screening large numbers of bacterial strains in order to determine which glycoconjugate structural features are conserved between strains of the same species. Provide the necessary structural information which, when coupled with developments in the rapidly expanding field of Rhizobium genetics, should lead to a clear understanding of the role of Rhizobium surface glycoconjugates in host/symbiont interactions. Progress is discussed.

  5. Products of Dark CO2 Fixation in Pea Root Nodules Support Bacteroid Metabolism 1

    PubMed Central

    Rosendahl, Lis; Vance, Carroll P.; Pedersen, Walther B.

    1990-01-01

    Products of the nodule cytosol in vivo dark [14C]CO2 fixation were detected in the plant cytosol as well as in the bacteroids of pea (Pisum sativum L. cv “Bodil”) nodules. The distribution of the metabolites of the dark CO2 fixation products was compared in effective (fix+) nodules infected by a wild-type Rhizobium leguminosarum (MNF 300), and ineffective (fix−) nodules of the R. leguminosarum mutant MNF 3080. The latter has a defect in the dicarboxylic acid transport system of the bacterial membrane. The 14C incorporation from [14C]CO2 was about threefold greater in the wild-type nodules than in the mutant nodules. Similarly, in wild-type nodules the in vitro phosphoenolpyruvate carboxylase activity was substantially greater than that of the mutant. Almost 90% of the 14C label in the cytosol was found in organic acids in both symbioses. Malate comprised about half of the total cytosol organic acid content on a molar basis, and more than 70% of the cytosol radioactivity in the organic acid fraction was detected in malate in both symbioses. Most of the remaining 14C was contained in the amino acid fraction of the cytosol in both symbioses. More than 70% of the 14C label found in the amino acids of the cytosol was incorporated in aspartate, which on a molar basis comprised only about 1% of the total amino acid pool in the cytosol. The extensive 14C labeling of malate and aspartate from nodule dark [14C]CO2 fixation is consistent with the role of phosphoenolpyruvate carboxlase in nodule dark CO2 fixation. Bacteroids from the effective wild-type symbiosis accumulated sevenfold more 14C than did the dicarboxylic acid transport defective bacteroids. The bacteroids of the effective MNF 300 symbiosis contained the largest proportion of the incorporated 14C in the organic acids, whereas ineffective MNF 3080 bacteroids mainly contained 14C in the amino acid fraction. In both symbioses a larger proportion of the bacteroid 14C label was detected in malate and aspartate

  6. Rhizobium sp. strain ORS571 ammonium assimilation and nitrogen fixation.

    PubMed Central

    Donald, R G; Ludwig, R A

    1984-01-01

    Among rhizobia studied, Rhizobium sp. strain ORS571 alone grew unambiguously on N2 as sole N source. In ORS571 , only the glutamine synthetase (GS)-glutamate synthase ( GOGAT ) pathway assimilated ammonium. However, ORS571 exhibited two unique physiological aspects of this pathway: ORS571 had only GS I, whereas all other Rhizobiaceae studied had both GS I and GS II, and both NADPH- and NADH-dependent GOGAT activities were present. ORS571 GS-affected and NADPH- GOGAT -affected mutant strains were defective in both ammonium assimilation (Asm-) and N2 fixation (Nif-) in culture and in planta ; NADH- GOGAT mutants were Asm- but Nif+. "Bacteroid" GS activity was essentially nil, suggesting symbiotic ammonium export. Physiological studies on effects of glutamine, ammonium, methionine sulfoximine, and diazo-oxo-norleucine on nitrogenase induction in culture implied a regulatory role for the intracellular glutamine pool. Images PMID:6144666

  7. Identification and manipulation of Rhizobium phytohormone genes

    SciTech Connect

    Ditta, G.S.

    1988-06-27

    The goal of this project was to determine whether phytohormone production by the gram-negative bacterium Rhizobium meliloti is required for successful modulation and symbiosis with alfalfa. specifically, we undertook the study of indoleacetic acid (IAA; auxin) production by R. meliloti and sought to create a mutant totally deficient in IAA biosynthesis. For many years it has been known that rhizobia are capable of synthesizing and excreting IAA, and it has often been suggested that this could be of importance for the initiation of root nodule development. Published work demonstrating the involvement of bacterial IAA genes in pathogenesis by Pseudomonas syringae and Agrobacterium tumefaciens further emphasized the need for this type of study in Rhizobium.

  8. Lipopolysaccharide O-Chain Core Region Required for Cellular Cohesion and Compaction of In Vitro and Root Biofilms Developed by Rhizobium leguminosarum

    PubMed Central

    Russo, Daniela M.; Abdian, Patricia L.; Posadas, Diana M.; Williams, Alan; Vozza, Nicolás; Giordano, Walter; Kannenberg, Elmar; Downie, J. Allan

    2014-01-01

    The formation of biofilms is an important survival strategy allowing rhizobia to live on soil particles and plant roots. Within the microcolonies of the biofilm developed by Rhizobium leguminosarum, rhizobial cells interact tightly through lateral and polar connections, forming organized and compact cell aggregates. These microcolonies are embedded in a biofilm matrix, whose main component is the acidic exopolysaccharide (EPS). Our work shows that the O-chain core region of the R. leguminosarum lipopolysaccharide (LPS) (which stretches out of the cell surface) strongly influences bacterial adhesive properties and cell-cell cohesion. Mutants defective in the O chain or O-chain core moiety developed premature microcolonies in which lateral bacterial contacts were greatly reduced. Furthermore, cell-cell interactions within the microcolonies of the LPS mutants were mediated mostly through their poles, resulting in a biofilm with an altered three-dimensional structure and increased thickness. In addition, on the root epidermis and on root hairs, O-antigen core-defective strains showed altered biofilm patterns with the typical microcolony compaction impaired. Taken together, these results indicate that the surface-exposed moiety of the LPS is crucial for proper cell-to-cell interactions and for the formation of robust biofilms on different surfaces. PMID:25416773

  9. MgtE From Rhizobium leguminosarum Is a Mg²⁺ Channel Essential for Growth at Low pH and N2 Fixation on Specific Plants.

    PubMed

    Hood, Graham; Karunakaran, Ramakrishnan; Downie, J Allan; Poole, Philip

    2015-12-01

    MgtE is predicted to be a Rhizobium leguminosarum channel and is essential for growth when both Mg²⁺ is limiting and the pH is low. N₂was only fixed at 8% of the rate of wild type when the crop legume Pisum sativum was inoculated with an mgtE mutant of R. leguminosarum and, although bacteroids were present, they were few in number and not fully developed. R. leguminosarum MgtE was also essential for N₂fixation on the native legume Vicia hirsuta but not when in symbiosis with Vicia faba. The importance of MgtE and the relevance of the contrasting phenotypes is discussed. PMID:26422403

  10. A carbonic anhydrase gene is induced in the nodule primordium and its cell-specific expression is controlled by the presence of Rhizobium during development.

    PubMed

    Coba de la Peña, T; Frugier, F; McKhann, H I; Bauer, P; Brown, S; Kondorosi, A; Crespi, M

    1997-03-01

    Under nitrogen starvation, Rhizobium meliloti is able to induce nitrogen-fixing nodules on alfalfa roots. Certain alfalfa cultivars spontaneously develop pseudonodules in the absence of bacteria. A transcript, Msca1, expressed in spontaneous and R. meliloti-induced nodules, that codes for a carbonic anhydrase (CA), an enzyme catalyzing the hydration of CO2 has been identified. This is the first CA gene cloned from a non-photosynthetic tissue in plants. Msca1 was activated initially in all cells of the bacterium-induced nodule primordium and was also induced by cytokinin treatment of alfalfa roots. The presence of CA enzymatic activity in different nodule types was demonstrated. Thus, Msca1 is a new early nodulin gene with a function possibly related to the increased amyloplast deposition of the dividing cortical cells. Msca1 transcripts were subsequently found mainly in a peripheral envelope of cells in developing and mature nodules. This novel pattern of gene expression is controlled by the presence of the bacterium inside the nodule. Sucrose synthase and phosphoenol pyruvate carboxylase (PEPC), other genes of the carbon fixation metabolism, were expressed in the same peripheral cells and even more strongly in the nitrogen-fixing region. Analysis of expression patterns of these genes indicated that early CA function may not be related to carbon fixation through PEPC. CA might be acting in pH regulation and/or CO2/HCO3-transport during nodule initiation. Thus, carbonic anhydrase may play different roles at several stages of nodule development and function. PMID:9107031

  11. Multiple antibiotic resistance in Rhizobium japonicum.

    PubMed

    Cole, M A; Elkan, G H

    1979-05-01

    A total of 48 strains of the soil bacterium Rhizobium japonicum were screened for their response to several widely used antibiotics. Over 60% of the strains were resistant to chloramphenicol, polymyxin B, and erythromycin, and 47% or more of the strains were resistant to neomycin and penicillin G, when tested by disk assay procedures. The most common grouping of resistances in strains was simultaneous resistance to tetracycline, penicillin G, neomycin, chloramphenicol, and streptomycin (25% of all strains tested). The occurrence of multiple drug resistance in a soil bacterium that is not a vertebrate pathogen suggests that chemotherapeutic use of antibiotics is not required for the development of multiple drug resistance. PMID:485137

  12. The development of plasmid-free strains of Agrobacterium tumefaciens by using incompatibility with a Rhizobium meliloti plasmid to eliminate pAtC58.

    PubMed

    Hynes, M F; Simon, R; Pühler, A

    1985-03-01

    Agrobacterium tumefaciens strains LBA275 and LBA290 were cured of their cryptic plasmid pAtC58 by the introduction of the Rhizobium meliloti plasmid pRme41a, which is incompatible with pAtC58. pRme41a and pTiC58, the resident Ti plasmid of LBA275, were subsequently eliminated by growth at supraoptimal temperature (40 degrees C). The resulting plasmid-free Agrobacterium strains, UBAPF1 and UBAPF2, have proved extremely useful for the study of Rhizobium plasmids. The loss of the cryptic plasmid pAtC58 has no effect on the tumor-forming ability of the Agrobacterium strains; when the Ti plasmid is present, normal tumors are formed on Kalanchoe daigremontiana. PMID:4001194

  13. Fine Structure of Bacteroids in Root Nodules of Vigna sinensis, Acacia longifolia, Viminaria juncea, and Lupinus angustifolius

    PubMed Central

    Dart, P. J.; Mercer, F. V.

    1966-01-01

    Dart, P. J. (University of Sydney, Sydney, Australia), and F. V. Mercer. Fine structure of bacteroids in root nodules of Vigna sinensis, Acacia longifolia, Viminaria juncea, and Lupinus angustifolius. J. Bacteriol. 91:1314–1319.—In nodules of Vigna sinensis, Acacia longifolia, and Viminaria juncea, membrane envelopes enclose groups of bacteroids. The bacteroids often contain inclusion granules and electron-dense bodies, expand little during development, and retain their rod form with a compact, central nucleoid area. The membrane envelope may persist around bacteroids after host cytoplasm breakdown. In nodules of Lupinus angustifolius, the membrane envelopes enclose only one or two bacteroids, which expand noticeably during development and change from their initial rod structure. Images PMID:5929757

  14. Characterization of Bacteroides forsythus isolates.

    PubMed

    Takemoto, T; Kurihara, H; Dahlen, G

    1997-06-01

    Fifteen Bacteroides forsythus strains freshly isolated from patients with periodontitis were used together with three collection strains and one type strain for characterization of growth on various media; determination of enzymatic profiles, antibiotic susceptibility profiles, 16S rRNA ribotypes, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) outer membrane protein profiles, and pathogenicity; and gas chromatography analysis by using a wound chamber model in rabbits. All strains were stimulated by N-acetylmuramic acid, while one strain needed a further supplement such as yeast extract for optimal growth. All strains showed trypsin-like activity. While 10 different ribotypes were found, the SDS-PAGE profiles revealed similar patterns for all strains. All strains were sensitive to penicillin G (MICs, <0.5 microg/ml), ampicillin (MICs, <1.0 microg/ml), amoxicillin (MICs, <0.38 microg/ml), metronidazole (MICs, <0.005 microg/ml), tetracycline (MICs, <0.19 microg/ml), doxycycline (MICs, 0.05 microg/ml), erythromycin (MICs, <0.4 microg/ml), and clindamycin (MICs, <0.016 microg/ml), while they were less sensitive to ciprofloxacin (MICs, <4 microg/ml). B. forsythus did not cause abscess formation by monoinoculation. B. forsythus coinoculated with Fusobacterium nucleatum ATCC 10953 caused abscess formation in 75% of rabbits, while it caused abscess formation in 100% of rabbits when it was coinoculated with Porphyromonas gingivalis FDC 381. In the case of the latter combination, four of six rabbits died of sepsis after 6 to 7 days, and P. gingivalis and B. forsythus were recovered from the heart blood at a proportion of 10:1. B. forsythus strains were highly virulent and invasive in combination with P. gingivalis. PMID:9163447

  15. Characterization of Bacteroides forsythus isolates.

    PubMed Central

    Takemoto, T; Kurihara, H; Dahlen, G

    1997-01-01

    Fifteen Bacteroides forsythus strains freshly isolated from patients with periodontitis were used together with three collection strains and one type strain for characterization of growth on various media; determination of enzymatic profiles, antibiotic susceptibility profiles, 16S rRNA ribotypes, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) outer membrane protein profiles, and pathogenicity; and gas chromatography analysis by using a wound chamber model in rabbits. All strains were stimulated by N-acetylmuramic acid, while one strain needed a further supplement such as yeast extract for optimal growth. All strains showed trypsin-like activity. While 10 different ribotypes were found, the SDS-PAGE profiles revealed similar patterns for all strains. All strains were sensitive to penicillin G (MICs, <0.5 microg/ml), ampicillin (MICs, <1.0 microg/ml), amoxicillin (MICs, <0.38 microg/ml), metronidazole (MICs, <0.005 microg/ml), tetracycline (MICs, <0.19 microg/ml), doxycycline (MICs, 0.05 microg/ml), erythromycin (MICs, <0.4 microg/ml), and clindamycin (MICs, <0.016 microg/ml), while they were less sensitive to ciprofloxacin (MICs, <4 microg/ml). B. forsythus did not cause abscess formation by monoinoculation. B. forsythus coinoculated with Fusobacterium nucleatum ATCC 10953 caused abscess formation in 75% of rabbits, while it caused abscess formation in 100% of rabbits when it was coinoculated with Porphyromonas gingivalis FDC 381. In the case of the latter combination, four of six rabbits died of sepsis after 6 to 7 days, and P. gingivalis and B. forsythus were recovered from the heart blood at a proportion of 10:1. B. forsythus strains were highly virulent and invasive in combination with P. gingivalis. PMID:9163447

  16. Modulation of endogenous indole-3-acetic acid biosynthesis in bacteroids within Medicago sativa nodules.

    PubMed

    Bianco, C; Senatore, B; Arbucci, S; Pieraccini, G; Defez, R

    2014-07-01

    To evaluate the dose-response effects of endogenous indole-3-acetic acid (IAA) on Medicago plant growth and dry weight production, we increased the synthesis of IAA in both free-living and symbiosis-stage rhizobial bacteroids during Rhizobium-legume symbiosis. For this purpose, site-directed mutagenesis was applied to modify an 85-bp promoter sequence, driving the expression of iaaM and tms2 genes for IAA biosynthesis. A positive correlation was found between the higher expression of IAA biosynthetic genes in free-living bacteria and the increased production of IAA under both free-living and symbiotic conditions. Plants nodulated by RD65 and RD66 strains, synthetizing the highest IAA concentration, showed a significant (up to 73%) increase in the shoot fresh weight and upregulation of nitrogenase gene, nifH, compared to plants nodulated by the wild-type strain. When these plants were analyzed by confocal microscopy, using an anti-IAA antibody, the strongest signal was observed in bacteroids of Medicago sativa RD66 (Ms-RD66) plants, even when they were located in the senescent nodule zone. We show here a simple system to modulate endogenous IAA biosynthesis in bacteria nodulating legumes suitable to investigate which is the maximum level of IAA biosynthesis, resulting in the maximal increase of plant growth. PMID:24814784

  17. The effect of environmental conditions on expression of Bacteroides fragilis and Bacteroides thetaiotaomicron C10 protease genes

    PubMed Central

    2012-01-01

    Background Bacteroides fragilis and Bacteroides thetaiotaomicron are members of the normal human intestinal microbiota. However, both organisms are capable of causing opportunistic infections, during which the environmental conditions to which the bacteria are exposed change dramatically. To further explore their potential for contributing to infection, we have characterized the expression in B. thetaiotaomicron of four homologues of the gene encoding the C10 cysteine protease SpeB, a potent extracellular virulence factor produced by Streptococcus pyogenes. Results We identified a paralogous set of genes (btp genes) in the B. thetaiotaomicron genome, that were related to C10 protease genes we recently identified in B. fragilis. Similar to C10 proteases found in B. fragilis, three of the B. thetaiotaomicron homologues were transcriptionally coupled to genes encoding small proteins that are similar in structural architecture to Staphostatins, protease inhibitors associated with Staphopains in Staphylococcus aureus. The expression of genes for these C10 proteases in both B. fragilis and B. thetaiotaomicron was found to be regulated by environmental stimuli, in particular by exposure to oxygen, which may be important for their contribution to the development of opportunistic infections. Conclusions Genes encoding C10 proteases are increasingly identified in operons which also contain genes encoding proteins homologous to protease inhibitors. The Bacteroides C10 protease gene expression levels are responsive to different environmental stimuli suggesting they may have distinct roles in the bacterial-host interaction. PMID:22943521

  18. SURVIVAL AND DETECTION OF 'BACTEROIDES' SPP., PROSPECTIVE INDICATOR BACTERIA

    EPA Science Inventory

    Preliminary experiments were performed to assess the use of intestinal Bacteroides spp. as indicators of fecal contamination of water. Viable counts of Bacteroides fragilis, an anaerobic bacterium, declined more rapidly than those of Escherichia coli and Streptococcus faecalis. H...

  19. Characterization of a Multidrug-Resistant, Novel Bacteroides Genomospecies

    PubMed Central

    Salipante, Stephen J.; Kalapila, Aley; Pottinger, Paul S.; Hoogestraat, Daniel R.; Cummings, Lisa; Duchin, Jeffrey S.; Sengupta, Dhruba J.; Pergam, Steven A.; Cookson, Brad T.

    2015-01-01

    Metronidazole- and carbapenem-resistant Bacteroides fragilis are rare in the United States. We isolated a multidrug-resistant anaerobe from the bloodstream and intraabdominal abscesses of a patient who had traveled to India. Whole-genome sequencing identified the organism as a novel Bacteroides genomospecies. Physicians should be aware of the possibility for concomitant carbapenem- and metronidazole-resistant Bacteroides infections. PMID:25529016

  20. Cloning and characterization of hydrogen uptake genes from Rhizobium leguminosarum.

    PubMed Central

    Leyva, A; Palacios, J M; Mozo, T; Ruiz-Argüeso, T

    1987-01-01

    A gene library of genomic DNA from the hydrogen uptake (Hup)-positive strain 128C53 of Rhizobium leguminosarum was constructed by using the broad-host-range mobilizable cosmid vector pLAFR1. The resulting recombinant cosmids contained insert DNA averaging 21 kilobase pairs (kb) in length. Two clones from the above gene library were identified by colony hybridization with DNA sequences from plasmid pHU1 containing hup genes of Bradyhizobium japonicum. The corresponding recombinant cosmids, pAL618 and pAL704, were isolated, and a region of about 28 kb containing the sequences homologous to B. japonicum hup-specific DNA was physically mapped. Further hybridization analysis with three fragments from pHU1 (5.9-kb HindIII, 2.9-kb EcoRI, and 5.0-kb EcoRI) showed that the overall arrangement of the R. leguminosarum hup-specific region closely parallels that of B. japonicum. The presence of functional hup genes within the isolated cosmid DNA was demonstrated by site-directed Tn5 mutagenesis of the 128C53 genome and analysis of the Hup phenotype of the Tn5 insertion strains in symbiosis with peas. Transposon Tn5 insertions at six different sites spanning 11 kb of pAL618 completely suppressed the hydrogenase activity of the pea bacteroids. Images PMID:2822654

  1. High-Resolution Transcriptomic Analyses of Sinorhizobium sp. NGR234 Bacteroids in Determinate Nodules of Vigna unguiculata and Indeterminate Nodules of Leucaena leucocephala

    PubMed Central

    Li, Yan; Tian, Chang Fu; Chen, Wen Feng; Wang, Lei; Sui, Xin Hua; Chen, Wen Xin

    2013-01-01

    The rhizobium-legume symbiosis is a model system for studying mutualistic interactions between bacteria and eukaryotes. Sinorhizobium sp. NGR234 is distinguished by its ability to form either indeterminate nodules or determinate nodules with diverse legumes. Here, we presented a high-resolution RNA-seq transcriptomic analysis of NGR234 bacteroids in indeterminate nodules of Leucaena leucocephala and determinate nodules of Vigna unguiculata. In contrast to exponentially growing free-living bacteria, non-growing bacteroids from both legumes recruited several common cellular functions such as cbb3 oxidase, thiamine biosynthesis, nitrate reduction pathway (NO-producing), succinate metabolism, PHB (poly-3-hydroxybutyrate) biosynthesis and phosphate/phosphonate transporters. However, different transcription profiles between bacteroids from two legumes were also uncovered for genes involved in the biosynthesis of exopolysaccharides, lipopolysaccharides, T3SS (type three secretion system) and effector proteins, cytochrome bd ubiquinol oxidase, PQQ (pyrroloquinoline quinone), cytochrome c550, pseudoazurin, biotin, phasins and glycolate oxidase, and in the metabolism of glutamate and phenylalanine. Noteworthy were the distinct expression patterns of genes encoding phasins, which are thought to be involved in regulating the surface/volume ratio of PHB granules. These patterns are in good agreement with the observed granule size difference between bacteroids from L. leucocephala and V. unguiculata. PMID:23936444

  2. Bacteroides sartorii is an earlier heterotypic synonym of Bacteroides chinchillae and has priority.

    PubMed

    Sakamoto, Mitsuo; Ohkuma, Moriya

    2012-06-01

    Strains of the recently proposed species Bacteroides chinchillae share more than 99.4 % 16S rRNA gene sequence similarity with the type strain of Bacteroides sartorii although these two species do not appear to be similar from their published descriptions. The aim of this study was to perform phenotypic and genetic analyses of both species to clarify their taxonomic position. B. chinchillae JCM 16497(T) exhibited high hsp60 gene sequence similarity with B. sartorii JCM 17136(T) (100 %) as well as B. chinchillae JCM 16498 (100 %). The hsp60 gene sequence analysis and levels of DNA-DNA relatedness observed demonstrated B. sartorii JCM 17136(T), B. chinchillae JCM 16497(T), and B. chinchillae JCM 16498 are members of a single species. Based on these data, we propose Bacteroides chinchillae as a later heterotypic synonym of Bacteroides sartorii. An emended description of B. sartorii is provided. PMID:21764984

  3. Interaction of Bacteroides fragilis and Bacteroides thetaiotaomicron with the kallikrein–kinin system

    PubMed Central

    Mörgelin, Matthias; Cooney, Jakki C.; Frick, Inga-Maria

    2011-01-01

    Many bacterial pathogens interfere with the contact system (kallikrein–kinin system) in human plasma. Activation of this system has two consequences: cleavage of high-molecular-mass kininogen (HK) resulting in release of the potent proinflammatory peptide bradykinin, and initiation of the intrinsic pathway of coagulation. In this study, two species of the Gram-negative anaerobic commensal organism Bacteroides, namely Bacteroides fragilis and Bacteroides thetaiotaomicron, were found to bind HK and fibrinogen, the major clotting protein, from human plasma as shown by immunoelectron microscopy and Western blot analysis. In addition, these Bacteroides species were capable of activating the contact system at its surface leading to a significant prolongation of the intrinsic coagulation time and also to the release of bradykinin. Members of the genus Bacteroides have been known to act as opportunistic pathogens outside the gut, with B. fragilis being the most common isolate from clinical infections, such as intra-abdominal abscesses and bacteraemia. The present results thus provide more insight into how Bacteroides species cause infection. PMID:21527472

  4. Molecular Investigations of Bacteroides as Microbial Source Tracking Tools in Southeast Louisiana Watersheds

    NASA Astrophysics Data System (ADS)

    Schulz, C. J.; Childers, G. W.; Engel, A. S.

    2006-12-01

    Microbial Source Tracking (MST) is a developing field that is gaining increased attention. MST refers to a host of techniques that discriminates among the origins of fecal material found in natural waters from different sources (e.g. human, livestock, and wildlife) by using microbial indicator species with specificity to only certain host organisms. The development of species-specific molecular markers would allow for better evaluation of public health risks and tracking of nutrient sources impacting a watershed. Although several MST methods have been reported with varying levels of success, few offer general applicability for natural waters due to spatial and temporal constraints associated with these methods. One group of molecular MST markers that show promise for broad environmental applications are molecular 16S rDNA probes for Bacteroides. This method is based on 16S rDNA detection directly from environmental samples without the need for a preliminary cultivation step. In this study we have expanded previous sampling efforts to compile a database of over 1000 partial 16S rRNA Bacteroides genes retrieved from the fecal material of 15 different host species (human, cat, dog, pig, kangaroo). To characterize survival of Bacteroides outside of the host, survival time of the Bacteroides marker was compared to that of E.coli under varying natural environmental conditions (temperature and salinity). Bacteroides displayed a survival curve with shouldering and tailing similar to that of E.coli, but log reduction times differed with treatment. In summary, MST marker stability was identified within host species and the overall Bacteroides community structure correlated to host diet, suggesting that detection of a Bacteroides community could confidently identify fecal contamination point sources. Natural water samples from southeast Louisiana were collected for MST including the Tangipahoa River watershed where the source of fecal contamination has been hotly debated. The

  5. Rapid glutamic acid decarboxylase test for identification of Bacteroides and Clostridium spp.

    PubMed Central

    Jilly, B J; Schreckenberger, P C; LeBeau, L J

    1984-01-01

    A rapid 4-h test for glutamic acid decarboxylase is described for the identification of certain anaerobic bacteria. The test substrate consisted of 1.0 g of L-glutamic acid, 0.3 ml of Triton X-155, and 0.05 g of bromcresol green sodium salt in 1 liter of water. The substrate was dispensed in 0.5-ml amounts into test tubes, and a turbid suspension was made with the test organism. The test was then incubated aerobically at 35 degrees C for 4 h. The development of a blue color was considered positive. A total of 345 strains of clinically isolated anaerobic bacteria were tested. All isolates of Bacteroides fragilis, Bacteroides thetaiotaomicron, Bacteroides uniformis. Clostridium perfringens, and Clostridium sordellii gave a positive reaction. Some isolates of Bacteroides distasonis and Bacteroides vulgatus were also positive. The use of this rapid test in conjunction with other rapid methods, such as the spot indol test, will enable laboratory workers to report these pathogens on the same day on which an inoculum of pure culture growth on agar is available. PMID:6376535

  6. Genome-wide transcript analysis of Bradyrhizobium japonicum bacteroids in soybean root nodules.

    PubMed

    Pessi, Gabriella; Ahrens, Christian H; Rehrauer, Hubert; Lindemann, Andrea; Hauser, Felix; Fischer, Hans-Martin; Hennecke, Hauke

    2007-11-01

    The transcriptome of endosymbiotic Bradyrhizobium japonicum bacteroids was assessed, using RNA extracted from determinate soybean root nodules. Results were compared with the transcript profiles of B. japonicum cells grown in either aerobic or microaerobic culture. Microoxia is a known trigger for the induction of symbiotically relevant genes. In fact, one third of the genes induced in bacteroids at day 21 after inoculation are congruent with those up-regulated in culture by a decreased oxygen concentration. The other induced genes, however, may be regulated by cues other than oxygen limitation. Both groups of genes provide a rich source for the possible discovery of novel functions related to symbiosis. Samples taken at different timepoints in nodule development have led to the distinction of genes expressed early and late in bacteroids. The experimental approach applied here is also useful for B. japonicum mutant analyses. As an example, we compared the transcriptome of wild-type bacteroids with that of bacteroids formed by a mutant defective in the RNA polymerase transcription factor sigma54. This led to a collection of hitherto unrecognized B. japonicum genes potentially transcribed in planta in a sigma54-dependent manner. PMID:17977147

  7. [Structure of surface glycoconjugates or Rhizobium species and their function in nitrogen fixation]; Progress report

    SciTech Connect

    1991-01-01

    Lipopolysaccharides (LPS) were isolated and purified from the surface of the Rhizobium species R. trifolii, R. leguminosarium and R. meliloti. A novel core tetrasaccharide and a trisaccharide required for nodulation were discovered. Several types of LPS from a single culture, inducible by nod gene inducers, were resolved by electrophoresis and chromatography. Other potential inducers are being investigated. At least three separate loci control LPS biosynthesis in R. meliloti. We maintain secreted, sulphated LPS involved in nodulation is attached to the cell surface, and have demonstrated sulphated, lipid-linked carbohydrates on the surface of R. meliloti. Antibodies to purified cell surface carbohydrate oligomers are being prepared. These antibodies will be used to screen bacteria, and also to identify cell surface changes associated with differentiation of a bacteria to a bacteroid.

  8. Effects of culture age on symbiotic infectivity of Rhizobium japonicum

    SciTech Connect

    Bhuvaneswari, T.V.; Mills, K.K.; Crist, D.K.; Evans, W.R.; Bauer, W.D.

    1983-01-01

    The infectivity of the soybean symbiont Rhizobium japonicum changed two- to fivefold with culture age for strains 110 ARS, 138 Str Spc, and 123 Spc, whereas culture age had relatively little effect on the infectivity of strains 83 Str and 61A76 Str. Infectivity was measured by determining the number of nodules which developed on soybean primary roots in the zone which contained developing and preemergent root hairs at the time of inoculation. Root cells in this region of the host root are susceptible to Rhizobium infection, but this susceptibility is lost during acropetal development and maturation of the root cells within a period of 4 to 6 h. Profiles of nodulation frequency at different locations on the root were not affected by the age of the R. japonicum cultures, indicating that culture age affected the efficiency of Rhizobium infection rather than how soon infections were initiated after inoculation. Inoculum dose-response experiments also indicated that culture age affected the efficiency of infection. Two strains, 61A76 Str and 83 Str, were relatively inefficient at all culture ages, particularly at low inoculum doses. Changes in infectivity with culture age were reasonably well correlated with changes in the proportion of cells in a culture capable of binding soybean lectin. Suspensions of R. japonicum in water were found to retain their viability and infectivity. 15 references, 6 figures, 2 tables.

  9. Effects of culture age on symbiotic infectivity of Rhizobium japonicum.

    PubMed

    Bhuvaneswari, T V; Mills, K K; Crist, D K; Evans, W R; Bauer, W D

    1983-01-01

    The infectivity of the soybean symbiont Rhizobium japonicum changed two- to fivefold with culture age for strains 110 ARS, 138 Str Spc, and 123 Spc, whereas culture age had relatively little effect on the infectivity of strains 83 Str and 61A76 Str. Infectivity was measured by determining the number of nodules which developed on soybean primary roots in the zone which contained developing and preemergent root hairs at the time of inoculation. Root cells in this region of the host root are susceptible to Rhizobium infection, but this susceptibility is lost during acropetal development and maturation of the root cells within a period of 4 to 6 h (T. V. Bhuvaneswari, B. G. Turgeon, and W. D. Bauer, Plant Physiol. 66:1027-1031, 1980). Profiles of nodulation frequency at different locations on the root were not affected by the age of the R. japonicum cultures, indicating that culture age affected the efficiency of Rhizobium infection rather than how soon infections were initiated after inoculation. Inoculum dose-response experiments also indicated that culture age affected the efficiency of infection. Two strains, 61A76 Str and 83 Str, were relatively inefficient at all culture ages, particularly at low inoculum doses. Changes in infectivity with culture age were reasonably well correlated with changes in the proportion of cells in a culture capable of binding soybean lectin. Suspensions of R. japonicum in water were found to retain their viability and infectivity. PMID:6681538

  10. Rhizobium meliloti Genes Encoding Catabolism of Trigonelline Are Induced under Symbiotic Conditions.

    PubMed

    Boivin, C.; Camut, S.; Malpica, C. A.; Truchet, G.; Rosenberg, C.

    1990-12-01

    Rhizobium meliloti trc genes controlling the catabolism of trigonelline, a plant secondary metabolite often abundant in legumes, are closely linked to nif-nod genes on the symbiotic megaplasmid pSym [Boivin, C., Malpica, C., Rosenberg, C., Denarie, J., Goldman, A., Fleury, V., Maille, M., Message, B., and Tepfer, D. (1989). In Molecular Signals in the Microbe-Plant Symbiotic and Pathogenic Systems. (Berlin: Springer-Verlag), pp. 401-407]. To investigate the role of trigonelline catabolism in the Rhizobium-legume interaction, we studied the regulation of trc gene expression in free-living and in endosymbiotic bacteria using Escherichia coli lacZ as a reporter gene. Experiments performed with free-living bacteria indicated that trc genes were organized in at least four transcription units and that the substrate trigonelline was a specific inducer for three of them. Noninducing trigonelline-related compounds such as betaines appeared to antagonize the inducing effect of trigonelline. None of the general or symbiotic regulatory genes ntrA, dctB/D, or nodD seemed to be involved in trigonelline catabolism. trc fusions exhibiting a low basal and a high induced [beta]-galactosidase activity when present on pSym were used to monitor trc gene expression in alfalfa tissue under symbiotic conditions. Results showed that trc genes are induced during all the symbiotic steps, i.e., in the rhizosphere, infection threads, and bacteroids of alfalfa, suggesting that trigonelline is a nutrient source throughout the Rhizobium-legume association. PMID:12354952

  11. USE OF BACTEROIDES PCR-BASED METHODS TO EXAMINE FECAL CONTAMINATION SOURCES IN TROPICAL COASTAL WATERS

    EPA Science Inventory

    Several library independent Microbial Source Tracking methods have been developed to rapidly determine the source of fecal contamination. Thus far, none of these methods have been tested in tropical marine waters. In this study, we used a Bacteroides 16S rDNA PCR-based...

  12. Conserved nodulation genes in Rhizobium meliloti and Rhizobium trifolii

    SciTech Connect

    Fisher, R.F.; Tu, J.K.; Long, S.R.

    1985-06-01

    Plasmids which contained wild-type or mutated Rhizobium meliloti nodulation (Nod) genes were introduced into Nod/sup -/ R. trifolii mutants ANU453 and ANU851 and tested for their ability to nodulate clover. Cloned wild-type and mutated R. meliloti Nod gene segments restored ANU851 to Nod/sup +/, with the exception of nodD mutants. Similarly, wild-type and mutant R. meliloti nod genes complemented ANU453 to Nod/sup +/, except for nod CII mutants. Thus, ANU851 identifies the equivalent of the R. meliloti nodD genes, and ANU453 specifies the equivalent of the R. meliloti nodCII genes. In addition, cloned wild-type R. trifolii nod genes were introduced into seven R. meliloti Nod/sup -/ mutants. All seven mutants were restored to Nod/sup +/ on alfalfa. Our results indicate that these genes represent common nodulation functions and argue for an allelic relationship between nod genes in R. meliloti and R. trifolii.

  13. Products of dark CO sub 2 fixation in pea root nodules support bacteroid metabolism. [Pisum sativum L

    SciTech Connect

    Rosendahl, L.; Pedersen, W.B. ); Vance, C.P. )

    1990-05-01

    Products of the nodule cytosol in vivo dark ({sup 14}C)CO{sub 2} fixation were detected in the plant cytosol as well as in the bacteroids of pea (Pisum sativum L. cv Bodil) nodules. The distribution of the metabolites of the dark CO{sub 2} fixation products was compared in effective (fix{sup +}) nodules infected by a wild-type Rhizobium leguminosarum (MNF 300), and ineffective (fix{sup {minus}}) nodules of the R. leguminosarum mutant MNF 3080. The latter has a defect in the dicarboxylic acid transport system of the bacterial membrane. The {sup 14}C incorporation from ({sup 14}C)CO{sub 2} was about threefold greater in the wild-type nodules than in the mutant nodules. Similarly, in wild-type nodules the in vitro phosphoenolpyruvate carboxylase activity was substantially greater than that of the mutant. Almost 90% of the {sup 14}C label in the cytosol was found in organic acids in both symbioses. The results indicate a central role for nodule cytosol dark CO{sub 2} fixation in the supply of the bacteroids with dicarboxylic acids.

  14. Activities of Nigerian chewing stick extracts against Bacteroides gingivalis and Bacteroides melaninogenicus.

    PubMed

    Rotimi, V O; Laughon, B E; Bartlett, J G; Mosadomi, H A

    1988-04-01

    The in vitro activities of extracts of Nigerian chewing sticks against Bacteroides gingivalis and B. melaninogenicus are presented. The greatest inhibitory action was produced by Serindeia werneckei, whereas Fagara zanthoxyloides produced no appreciable inhibitory effect. A generally good correlation was found between the killing curves and MICs. Only extracts of Anogeissus leiocarpus showed acute toxicity in mice. PMID:2897830

  15. Activities of Nigerian chewing stick extracts against Bacteroides gingivalis and Bacteroides melaninogenicus.

    PubMed Central

    Rotimi, V O; Laughon, B E; Bartlett, J G; Mosadomi, H A

    1988-01-01

    The in vitro activities of extracts of Nigerian chewing sticks against Bacteroides gingivalis and B. melaninogenicus are presented. The greatest inhibitory action was produced by Serindeia werneckei, whereas Fagara zanthoxyloides produced no appreciable inhibitory effect. A generally good correlation was found between the killing curves and MICs. Only extracts of Anogeissus leiocarpus showed acute toxicity in mice. PMID:2897830

  16. Bacteroides plebeius sp. nov. and Bacteroides coprocola sp. nov., isolated from human faeces.

    PubMed

    Kitahara, Maki; Sakamoto, Mitsuo; Ike, Masako; Sakata, Shinji; Benno, Yoshimi

    2005-09-01

    Nine strains of Gram-negative, anaerobic rod were isolated from human faeces. Based on phylogenetic analysis and specific phenotypic characteristics, these strains were included within the Bacteroides cluster and were divided into two clusters. Strains from the two clusters showed 16S rRNA gene sequence similarities of 90.4 and 92.7% to the nearest recognized species, Bacteroides vulgatus. The strains also formed two clusters exhibiting a 16S rRNA gene sequence divergence of approximately 6%. DNA-DNA hybridization studies confirmed that the two novel strain clusters were distinct from each other. Based on the phenotypic and phylogenetic findings, two novel species, Bacteroides plebeius sp. nov. and Bacteroides coprocola sp. nov., are proposed, each representing one of the two strain clusters. The DNA G+C content of the type strains were 43.9 mol% for B. plebeius (M12(T)=JCM 12973(T)=DSM 17135(T)) and 42.4 mol% for B. coprocola (M16(T)=JCM 12979(T)=DSM 17136(T)). PMID:16166722

  17. The arginine deiminase pathway in Rhizobium etli: DNA sequence analysis and functional study of the arcABC genes.

    PubMed Central

    D'Hooghe, I; Vander Wauven, C; Michiels, J; Tricot, C; de Wilde, P; Vanderleyden, J; Stalon, V

    1997-01-01

    Sequence analysis upstream of the Rhizobium etli fixLJ homologous genes revealed the presence of three open reading frames homologous to the arcABC genes of Pseudomonas aeruginosa. The P. aeruginosa arcABC genes code for the enzymes of the arginine deiminase pathway: arginine deiminase, catabolic ornithine carbamoyltransferase (cOTCase), and carbamate kinase. OTCase activities were measured in free-living R. etli cells and in bacteroids isolated from bean nodules. OTCase activity in free-living cells was observed at a different pH optimum than OTCase activity in bacteroids, suggesting the presence of two enzymes with different characteristics and different expression patterns of the corresponding genes. The characteristics of the OTCase isolated from the bacteroids were studied in further detail and were shown to be similar to the properties of the cOTCase of P. aeruginosa. The enzyme has a pH optimum of 6.8 and a molecular mass of approximately 450 kDa, is characterized by a sigmoidal carbamoyl phosphate saturation curve, and exhibits a cooperativity for carbamoyl phosphate. R. etli arcA mutants, with polar effects on arcB and arcC, were constructed by insertion mutagenesis. Bean nodules induced by arcA mutants were still able to fix nitrogen but showed a significantly lower acetylene reduction activity than nodules induced by the wild type. No significant differences in nodule dry weight, plant dry weight, and number of nodules were found between the wild type and the mutants. Determination of the OTCase activity in extracts from bacteroids revealed a strong decrease in activity of this enzyme in the arcA mutant compared to the wild-type strain. Finally, we observed that expression of an R. etli arcA-gusA fusion was strongly induced under anaerobic conditions. PMID:9393705

  18. Bacteroides-associated pylephlebitis in a patient with strongyloidiasis.

    PubMed

    Stone, Neil R H; Martin, Thomas; Biswas, Jason; Barrett, Jessica; Hickish, Tom; Dasgupta, Dhruba; Newsholme, William

    2015-02-01

    Strongyloidiasis is associated with Gram-negative bacteremia. Septic portal vein thrombosis or pylephlebitis is a rare but serious complication of intra-abdominal infection, and it is often associated with Bacteroides bacteremia. We present the first report of pylephlebitis with Bacteroides bacteremia associated with underlying Strongyloides stercoralis infection and briefly review the management of septic portal vein thrombosis. PMID:25510718

  19. Effect of Protein Additives on Acetylene Reduction (Nitrogen Fixation) by Rhizobium in the Presence and Absence of Soybean Cells 1

    PubMed Central

    Anderson, Stephen J.; Phillips, Donald A.

    1976-01-01

    The effect of protein additives on acetylene reduction (N2 fixation) by Rhizobium associated with soybean cells (Glycine max [L.] Merr.) in vitro was studied. Acetylene reduction was promoted on the basal medium supplemented with 1.4 mg of N/ml supplied as aqueous extracts of hexane-extracted soybean, red kidney beans (Phaseolus vulgaris L.), or peas (Pisum sativum L.). Commercial samples of α-casein, or bovine serum albumin also promoted acetylene reduction at a concentration of 1.4 mg of N/ml of basal medium, but egg albumin supplying an equal amount of nitrogen to the basal medium completely suppressed acetylene reduction. Autoclaving the aqueous extract of hexane-extracted soybean meal had no effect on its ability to promote acetylene reduction. The presence of 40 mm succinate decreased acetylene reduction with leguminous proteins supplying 1.4 mg of N/ml but promoted acetylene reduction by Rhizobium 32H1-soybean cell associations on media containing α-casein, bovine serum albumin, or egg albumin suppling 1.4 mg of N/ml. Similar results were obtained with both cowpea Rhizobium 32H1 and Rhizobium japonicum 61A96. Pure cultures of Rhizobium 32H1 developed acetylene-reducing activity in the presence of soybean extract on basal agar medium and in vermiculite supplied with N-free mineral salts plus crude soybean meal. The results suggest that in certain situations, free living Rhizobium may reduce N2 under field conditions. PMID:16659592

  20. The symbiovar trifolii of Rhizobium bangladeshense and Rhizobium aegyptiacum sp. nov. nodulate Trifolium alexandrinum in Egypt.

    PubMed

    Shamseldin, Abdelaal; Carro, Lorena; Peix, Alvaro; Velázquez, Encarna; Moawad, Hassan; Sadowsky, Michael J

    2016-06-01

    In the present work we analyzed the taxonomic status of several Rhizobium strains isolated from Trifolium alexandrinum L. nodules in Egypt. The 16S rRNA genes of these strains were identical to those of Rhizobium bangladeshense BLR175(T) and Rhizobium binae BLR195(T). However, the analyses of recA and atpD genes split the strains into two clusters. Cluster II strains are identified as R. bangladeshense with >98% similarity values in both genes. The cluster I strains are phylogenetically related to Rhizobium etli CFN42(T) and R. bangladeshense BLR175(T), but with less than 94% similarity values in recA and atpD genes. DNA-DNA hybridization analysis showed 42% and 48% average relatedness between the strain 1010(T) from cluster I with respect to R. bangladeshense BLR175(T) and R. etli CFN42(T), respectively. Phenotypic characteristics of cluster I strains also differed from those of their closest related Rhizobium species. Analysis of the nodC gene showed that the strains belong to two groups within the symbiovar trifolii which was identified in Egypt linked to the species R. bangladeshense. Based on the genotypic and phenotypic characteristics, the group I strains belong to a new species for which the name Rhizobium aegyptiacum sp. nov. (sv. trifolii) is proposed, with strain 1010(T) being designated as the type strain (= USDA 7124(T)=LMG 29296(T)=CECT 9098(T)). PMID:27236564

  1. Morphogenetic expression of Bacteroides nodosus fimbriae in Pseudomonas aeruginosa.

    PubMed Central

    Mattick, J S; Bills, M M; Anderson, B J; Dalrymple, B; Mott, M R; Egerton, J R

    1987-01-01

    Type 4 fimbriae are found in a range of pathogenic bacteria, including Bacteroides nodosus, Moraxella bovis, Neisseria gonorrhoeae, and Pseudomonas aeruginosa. The structural subunits of these fimbriae all contain a highly conserved hydrophobic amino-terminal sequence preceding a variable hydrophilic carboxy-terminal region. We show here that recombinant P. aeruginosa cells containing the B. nodosus fimbrial subunit gene under the control of a strong promoter (pL, from bacteriophage lambda) produced large amounts of fimbriae that were structurally and antigenically indistinguishable from those produced by B. nodosus. This was demonstrated by fimbrial isolation and purification, electrophoretic and Western transfer analyses, and immunogold labeling and electron microscopy. These results suggest that type 4 fimbriated bacteria use a common mechanism for fimbrial assembly and that the structural subunits are interchangeable, thereby providing a basis for the development of multivalent vaccines. Images PMID:2878919

  2. [The first metronidazole-resistant Bacteroides species isolated at Marmara University Hospital: Bacteroides thetaiotaomicron].

    PubMed

    Toprak Ülger, Nurver; Sayın, Elvan; Soyad, Ad; Dane, Faysal; Söyletir, Güner

    2013-10-01

    Bacteroides species, the predominant constituents of the human intestinal microbiota can cause serious intraabdominal and postoperative wound infections and bacteremia. Moreover, these bacteria are more resistant to antimicrobial agents than the other anaerobes. The limited number of the antimicrobials, such as carbapenems, beta-lactam/beta-lactamase inhibitors and nitroimidazoles are highly effective in eliminating Bacteroides. However, a few metronidazole-resistant isolates have been reported from several countries recently. The nim genes (nim A-G) are suggested to be responsible for the majority of the metronidazole resistance. Here, we describe a metronidazole-resistant Bacteroides thetaiotaomicron isolated from a blood culture. A gram-negative obligate anaerobic rod was isolated from the postoperative 5th day blood culture of a 62-year-old male patient with adenocarcinoma of the pancreas head. The strain was identified as B.thetaiotaomicron by using a combination of conventional tests and commercially available biochemical kits. Antimicrobial susceptibility testing was performed by agar dilution method. The resistance genes were investigated by means of PCR using specific primer pairs for nim gene. The purified PCR product was sequenced and analyzed by comparison of the consensus sequences with GenBank sequences. The MIC for metronidazole was 16 mg/L. Although the strain was intermediate according the CLSI criteria, it was resistant (> 4 mg/L) according to EUCAST criteria. The isolate was nim gene positive, and nucleotide sequencing of the PCR product shared 100% similarity with nimE gene (emb |AM042593.1 |). On the other hand the isolate was susceptible to carbapenems and sulbactam-ampicillin. Following administration of ampicillin-sulbactam, the patient's fever disappeared after 24 hours. The clinical condition improved considerably and he was discharged at day 8. The patient was followed up at the medical oncology clinic; however he died due to disease

  3. Structural Characterization of the Primary O-antigenic Polysaccharide of the Rhizobium leguminosarum 3841 Lipopolysaccharide and Identification of a New 3-Acetimidoylamino-3-deoxyhexuronic Acid Glycosyl Component

    PubMed Central

    Forsberg, L. Scott; Carlson, Russell W.

    2008-01-01

    Rhizobium are Gram-negative bacteria that survive intracellularly, within host membrane-derived plant cell compartments called symbiosomes. Within the symbiosomes the bacteria differentiate to bacteroids, the active form that carries out nitrogen fixation. The progression from free-living bacteria to bacteroid is characterized by physiological and morphological changes at the bacterial surface, a phase shift with an altered array of cell surface glycoconjugates. Lipopolysaccharides undergo structural changes upon differentiation from the free living to the bacteroid (intracellular) form. The array of carbohydrate structures carried on lipopolysaccharides confer resistance to plant defense mechanisms and may serve as signals that trigger the plant to allow the infection to proceed. We have determined the structure of the major O-polysaccharide (OPS) isolated from free living Rhizobium leguminosarum 3841, a symbiont of Pisum sativum, using chemical methods, mass spectrometry, and NMR spectroscopy analysis. The OPS is composed of several unusual glycosyl residues, including 6-deoxy-3-O-methyl-d-talose and 2-acetamido-2deoxy-l-quinovosamine. In addition, a new glycosyl residue, 3-acetimidoylamino-3-deoxy-d-gluco-hexuronic acid was identified and characterized, a novel hexosaminuronic acid that does not have an amino group at the 2-position. The OPS is composed of three to four tetrasaccharide repeating units of →4)-β-dGlcp3NAmA-(1→4)-[2-O-Ac-3-O-Me-α-d-6dTalp-(1→3)]-α-l-Fucp-(1→3)-α-l-QuipNAc-(1→. The unique 3-amino hexuronate residue, rhizoaminuronic acid, is an attractive candidate for selective inhibition of OPS synthesis. PMID:18387959

  4. Localization of aluminum in soybean bacteroids and seeds

    SciTech Connect

    Roth, L.E.; Dunlap, J.R.; Stacey, G.

    1987-10-01

    Aluminum, long known to be detrimental to soybean productivity, was localized in the polyphosphate granules (PPG) of bacteroids in root nodules of soybean plants. By using energy-dispersive X-ray analysis, bacteroids in early infections were shown to have typical PPG constituents. However, in PPG in older infections and after the bacteroids were digested intracellularly, aluminum was also detected. These results indicate that aluminum accumulates in PPG after a period when organisms have been resident in host cells and that high levels of aluminum were present in the bacteroids at the time of their demise. At least some of the aluminum in these laboratory-grown plants could have come from the seeds used.

  5. Characterization of the cycHJKL genes involved in cytochrome c biogenesis and symbiotic nitrogen fixation in Rhizobium leguminosarum.

    PubMed Central

    Delgado, M J; Yeoman, K H; Wu, G; Vargas, C; Davies, A E; Poole, R K; Johnston, A W; Downie, J A

    1995-01-01

    Mutants of Rhizobium leguminosarum bv. viciae unable to respire via the cytochrome aa3 pathway were identified by the inability to oxidize N,N'-dimethyl-p-phenylenediamine. Two mutants which were complemented by cosmid pIJ1942 from an R. leguminosarum clone bank were identified. Although pea nodules induced by these mutants contained many bacteroids, no symbiotic nitrogen fixation was detected. Heme staining of cellular proteins revealed that all cytochrome c-type heme proteins were absent. These mutants lacked spectroscopically detectable cytochrome c, but cytochromes aa3 and d were present, the latter at a higher-than-normal level. DNA sequence analysis of complementing plasmids revealed four apparently cotranscribed open reading frames (cycH, cycJ, cycK, and cycL). CycH, CycJ, CycK, and CycL are homologous to Bradyrhizobium japonicum and Rhizobium meliloti proteins thought to be involved in the attachment of heme to cytochrome c apoproteins; CycK and CycL are also homologous to the Rhodobacter capsulatus ccl1 and ccl2 gene products and the Escherichia coli nrfE and nrfF gene products involved in the assembly of c-type cytochromes. The absence of cytochrome c heme proteins in these R. leguminosarum mutants is consistent with the view that the cycHJKL operon could be involved in the attachment of heme to apocytochrome c. PMID:7665469

  6. Rapid and correct identification of intestinal Bacteroides spp. with chromosomal DNA probes by whole-cell dot blot hybridization

    SciTech Connect

    Morotomi, M.; Ohno, T.; Mutai, M.

    1988-05-01

    A dot blot hybridization procedure with /sup 32/P-labeled whole chromosomal DNA of the type strains as probes was developed as a rapid and simple method for identification of intestinal Bacteroides species. Bacterial cells were fixed onto membrane filters by slight suction, treated with 0.5 N NaOH, and hybridized with these probes. Of 65 Bacteroides strains isolated from 19 human fecal specimens, which were identified as B. fragilis, B. thetaiotaomicron, B. ovatus, B. caccae, B. uniformis, B. stercoris, B. vulgatus, B. distasonis, and B. merdae by conventional phenotypic characterization, 62 (95%) were correctly identified with this hybridization procedure.

  7. Polyethylene glycol-facilitated transformation of Bacteroides fragilis with plasmid DNA

    SciTech Connect

    Smith, C.J.

    1985-10-01

    A method for the transformation of Bacteroides fragilis with plasmid DNA was developed by using the clindamycin resistance plasmid pBFTM10 as the source of transforming DNA. The method was technically simple to perform and resulted in an average of 4.2 x 10/sup 3/ tranformants per ..mu..g of pBFTM10 added. A method for the preparation of frozen competent cells is also described.

  8. Host-symbiont interactions-V. The structure of acidic extracellular polysaccharides secreted by Rhizobium leguminosarum and Rhizobium trifolii

    SciTech Connect

    Robertsen, B.K.; Aman, P.; Darvill, A.G.; McNeil, M.; Albersheim, P.

    1981-01-01

    The sequence of the glycosyl residues and the anomeric configurations of the glycosl linkages of the acidic polysaccharides secreted by Rhizobium leguminosarum 128c53, Rhizobium leguminosarum 128c63, Rhizobium trifolii NA30, and Rhizobium trifolii 0403 have been determined. Each of the glycosyl residues of these polysaccharides was determined to be in the D configuration and in the pyranose ring form. These results add support to the proposal that R. leguminosarum and R. trifolii have a particularly close genetic relationship. The significance of these results with regard to the possible function of these polysaccharides in the nodulation process is discussed. (JMT)

  9. Bacteroides gingivalis and Bacteroides intermedius recognize different sites on human fibrinogen

    SciTech Connect

    Lantz, M.S.; Allen, R.D.; Bounelis, P.; Switalski, L.M.; Hook, M. )

    1990-02-01

    Bacteroides (Porphyromonas) gingivalis and Bacteroides (Porphyromonas) intermedius have been implicated in the etiology of human periodontal diseases. These organisms are able to bind and degrade human fibrinogen, and these interactions may play a role in the pathogenesis of periodontal disease. In attempts to map the bacterial binding sites along the fibrinogen molecule, we have found that strains of B. gingivalis and B. intermedius, respectively, recognize spatially distant and distinct sites on the fibrinogen molecule. Isolated reduced and alkylated alpha-, beta-, and gamma-fibrinogen chains inhibited binding of 125I-fibrinogen to both Bacteroides species in a concentration-dependent manner. Plasmin fragments D and to some extent fragment E, however, produced a concentration-dependent inhibition of 125I-fibrinogen binding to B. intermedius strains but did not affect binding of 125I-fibrinogen to B. gingivalis strains. Radiolabeled fibrinogen chains and fragments were compared with 125I-fibrinogen with respect to specificity and reversibility of binding to bacteria. According to these criteria, gamma chain most closely resembled the native fibrinogen molecule in behavior toward B. gingivalis strains and fragments D most closely resembled fibrinogen in behavior toward B. intermedius strains. The ability of anti-human fibrinogen immunoglobulin G (IgG) to inhibit binding of 125I-fibrinogen to B. intermedius strains was greatly reduced by absorbing the IgG with fragments D. Absorbing the IgG with fragments D had no effect on the ability of the antibody to inhibit binding of 125I-fibrinogen to B. gingivalis strains. A purified staphylococcal fibrinogen-binding protein blocked binding of 125I-fibrinogen to B. intermedius strains but not to B. gingivalis strains.

  10. A Novel Tightly Regulated Gene Expression System for the Human Intestinal Symbiont Bacteroides thetaiotaomicron

    PubMed Central

    Horn, Nikki; Carvalho, Ana L.; Overweg, Karin; Wegmann, Udo; Carding, Simon R.; Stentz, Régis

    2016-01-01

    There is considerable interest in studying the function of Bacteroides species resident in the human gastrointestinal (GI)-tract and the contribution they make to host health. Reverse genetics and protein expression techniques, such as those developed for well-characterized Escherichia coli cannot be applied to Bacteroides species as they and other members of the Bacteriodetes phylum have unique promoter structures. The availability of useful Bacteroides-specific genetic tools is therefore limited. Here we describe the development of an effective mannan-controlled gene expression system for Bacteroides thetaiotaomicron containing the mannan-inducible promoter–region of an α-1,2-mannosidase gene (BT_3784), a ribosomal binding site designed to modulate expression, a multiple cloning site to facilitate the cloning of genes of interest, and a transcriptional terminator. Using the Lactobacillus pepI as a reporter gene, mannan induction resulted in an increase of reporter activity in a time- and concentration-dependent manner with a wide range of activity. The endogenous BtcepA cephalosporinase gene was used to demonstrate the suitability of this novel expression system, enabling the isolation of a His-tagged version of BtCepA. We have also shown with experiments performed in mice that the system can be induced in vivo in the presence of an exogenous source of mannan. By enabling the controlled expression of endogenous and exogenous genes in B. thetaiotaomicron this novel inducer-dependent expression system will aid in defining the physiological role of individual genes and the functional analyses of their products. PMID:27468280

  11. Nutritional features of Bacteroides fragilis subsp. fragilis.

    PubMed

    Varel, V H; Bryant, M P

    1974-08-01

    Studies of three reference strains of Bacteroides fragilis subsp. fragilis showed that they grow well in a minimal defined medium containing glucose, hemin, vitamin B(12), minerals, bicarbonate-carbon dioxide buffer, NH(4)Cl, and sulfide. The vitamin B(12) requirement of 0.1 ng/ml was replaced with 7.5 mug of methionine. Cysteine or sulfide was an excellent source of sulfur, thioglycolate was a poor source, and thiosulfate, methionine, beta-mercaptoethanol, dithiothreitol, sulfate, or sulfite did not serve as sole sources of sulfur. Neither single amino acids, nitrate, urea, nor a complex mixture of L-amino acids or peptides effectively replaced ammonia as the nitrogen source. Comparative studies with a few strains of other subspecies of B. fragilis including B. fragilis subsp. vulgatus, B. fragilis subsp. thetaiotaomicron, and B. fragilis subsp. distasonis indicate that they exhibit similar growth responses in the minimal medium. A single strain of B. fragilis subsp. ovatus required other materials. The results indicate the great biosynthetic ability of these organisms and suggest that, in their ecological niche within the large intestine, many nutrients such as amino acids are in very low supply, whereas materials such as ammonia, heme, and vitamin B(12), or related compounds, must be available during much of the time. PMID:4853401

  12. Design and evaluation of Bacteroides DNA probes for the specific detection of human fecal pollution.

    PubMed Central

    Kreader, C A

    1995-01-01

    Because Bacteroides spp. are obligate anaerobes that dominate the human fecal flora, and because some species may live only in the human intestine, these bacteria might be useful to distinguish human from nonhuman sources of fecal pollution. To test this hypothesis, PCR primers specific for 16S rRNA gene sequences of Bacteroides distasonis, B. thetaiotaomicron, and B. vulgatus were designed. Hybridization with species-specific internal probes was used to detect the intended PCR products. Extracts from 66 known Bacteroides strains, representing 10 related species, were used to confirm the specificity of these PCR-hybridization assays. To test for specificity in feces, procedures were developed to prepare DNA of sufficient purity for PCR. Extracts of feces from 9 humans and 70 nonhumans (cats, dogs, cattle, hogs, horses, sheep, goats, and chickens) were each analyzed with and without an internal positive control to verify that PCR amplification was not inhibited by substances in the extract. In addition, serial dilutions from each extract that tested positive were assayed to estimate the relative abundance of target Bacteroides spp. in the sample. Depending on the primer-probe set used, either 78 or 67% of the human fecal extracts tested had high levels of target DNA. On the other hand, only 7 to 11% of the nonhuman extracts tested had similarly high levels of target DNA. An additional 12 to 20% of the nonhuman extracts had levels of target DNA that were 100- to 1,000-fold lower than those found in humans.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7538270

  13. Design and evaluation of Bacteroides DNA probes for the specific detection of human fecal pollution

    SciTech Connect

    Kreader, C.A.

    1995-04-01

    Because Bacteroides spp. are obligate anaerobes that dominate the human fecal flora, and because some species may live only in the human intestine, these bacteria might be useful to distinguish human from nonhuman sources of fecal pollution. To test this hypothesis, PCR primers specific for 16S rRNA gene sequences of Bacteroides distasonis, B. thetaiotaomicron, and B. vulgatus were designed. Hybridization with species-specific internal probes was used to detect the intended PCR products. Extracts from 66 known Bacteroides strains, representing 10 related species, were used to confirm the specificity of these PCR-hybridization assays. To test for specificity in feces, procedures were developed to prepare DNA of sufficient purity for PCR. Extracts of feces from 9 humans and 70 nonhumans (cats, dogs, cattle, hogs, horses, sheep, goats, and chickens) were each analyzed with and without an internal positive control to verify that PCR amplification was not inhibited by substances in the extract. In addition, serial dilutions from each extract that tested positive were assayed to estimate the relative abundance of target Bacteroides spp. in the sample. Depending on the primer-probe set used, either 78 or 67% of the human fecal extracts tested had high levels of target DNA. On the other hand, only 7 to 11% of the nonhuman extracts tested had similarly high levels of target DNA. An additional 12 to 20% of the nonhuman extracts had levels of target DNA that were 100- to 1,000-fold lower than those found in humans. Although the B. vulgatus probes detected high levels of their target DNA in most of the house pets, similarly high levels of target DNA were found only in a few individuals from other groups of nonhumans. Therefore, the results indicate that these probes can distinguish human from non human feces in many cases. 50 refs., 5 figs., 2 tabs.

  14. Cytotoxic and immunostimulatory effects of Bacteroides cell products.

    PubMed

    Fotos, P G; Lewis, D M; Gerencser, V F; Gerencser, M A

    1990-09-01

    The etiologic role of Bacteroides in both periodontal and periapical infections has been well documented, with current interest focusing on the specific pathogenic mechanisms involved. The effects of cell fractions derived from Bacteroides gingivalis (BG), Bacteroides intermedius (BI), and Bacteroides asaccharolyticus (BA) have been studied in vitro through: an assessment of the direct cytotoxic effects on human gingival fibroblasts using a tetrazolium dye reduction assay, an evaluation of murine lymphocyte stimulation and interleukin-1 release, and the induction of human lymphocyte-mediated cytotoxicity. Both BG and BI stimulated interleukin-1 release (P less than 0.001), while BA, a nonoral organism, was not significantly active in this respect. Only BG sonicates were able to induce lymphocyte-mediated cytotoxicity (P less than 0.005). All three Bacteroides species demonstrated direct cytotoxic effects on cultured gingival fibroblasts, and these effects were related to the relative protein content and endotoxin activity of the sonicate preparations for each organism. These data show that BG and BI possess factors which may enhance their virulence through activities not shared with BA. PMID:2250226

  15. Amino Acid and Vitamin Requirements of Several Bacteroides Strains

    PubMed Central

    Quinto, Grace

    1966-01-01

    Nutritional studies were performed on nine Bacteroides strains, by use of the methodology and media of anaerobic rumen microbiology. Ristella perfoetens CCI required l-arginine hydrochloride, l-tryptophan, l-leucine, l-histidine hydrochloride, l-cysteine hydrochloride, dl-valine, dl-tyrosine, and the vitamin calcium-d-pantothenate, since scant turbidity developed in media without these nutrients. R. perfoetens was stimulated by glycine, dl-lysine hydrochloride, dl-isoleucine, l-proline, l-glutamic acid, dl-alanine, dl-phenylalanine, dl-methionine, and the vitamins nicotinamide and p-aminobenzoic acid, since maximal turbidity developed more slowly in media without these nutrients than in complete medium. Medium A-23, which was devised for R. perfoetens, contained salts, 0.0002% nicotinamide and calcium d-pantothenate, 0.00001% p-aminobenzoic acid, 0.044% l-tryptophan, 0.09% l-glutamic acid, and 0.1% of the other 13 amino acids listed above. Zuberella clostridiformis and seven strains of R. pseudoinsolita did not require vitamins, and showed no absolute requirement for any one amino acid. Various strains produced maximal turbidity more slowly in media deficient in l-proline, glycine, l-glutamic acid, dl-serine, l-histidine hydrochloride, dl-alanine, or l-cysteine hydrochloride, than in complete medium. These eight strains grew optimally in medium A-23 plus 0.1% dl-serine but without vitamins. PMID:16349673

  16. (Analysis of the Rhizobium meliloti surface):

    SciTech Connect

    Signer, E.R.

    1988-03-03

    We have identified a number of genes in Rhizobium meliloti that affect outer membrane lipopolysaccharides (LPS). These include three genes defined by mutants with different patterns of resistance to a panel of bacteriophages, of which Class 2 and 3 are closely linked to each other but not to Class 1 or 4;another gene, closely linked to Class 2 and 3, defined only by its ability to suppress Class 1 defects;and three genes, unlinked to each other, defined by mutants with increased sensitivity to deoxycholate. Of the mutants that define these genes, only those in Class 2 have a clear effect on alfalfa symbiosis, having a Fix phenotype.

  17. An osmoregulated dipeptide in stressed Rhizobium meliloti.

    PubMed Central

    Smith, L T; Smith, G M

    1989-01-01

    One common mechanism of cellular adaptation to osmotic stress is the accumulation of organic solutes in the cytosol. We have used natural-abundance 13C nuclear magnetic resonance to identify all organic solutes that accumulate to significant levels in Rhizobium meliloti. Our studies led to the discovery of a new dipeptide, N-acetylglutaminylglutamine amide (NAGGN), which is accumulated during osmotic stress. Only rarely have peptides been shown to function in bacteria, and furthermore, this is the first example of a peptide playing a role in osmoregulation. Evidence for the biological role of NAGGN in osmotic-stress protection is presented. PMID:2768187

  18. Variability among Rhizobium Strains Originating from Nodules of Vicia faba.

    PubMed

    van Berkum, P; Beyene, D; Vera, F T; Keyser, H H

    1995-07-01

    Rhizobium strains from nodules of Vicia faba were diverse in plasmid content and serology. Results of multilocus gel electrophoresis and restriction fragment length polymorphism indicated several deep chromosomal lineages among the strains. Linkage disequilibrium among the chromosomal types was detected and may have reflected variation of Rhizobium strains in the different geographical locations from which the strains originated. An investigation of pea strains with antibodies prepared against fava bean strains and restriction fragment length polymorphism analyses, targeting DNA regions coding for rRNA and nodulation, indicated that Rhizobium strains from V. faba nodules were distinguishable from those from Pisum sativum, V. villosa, and Trifolium spp. PMID:16535075

  19. Growth of fast- and slow-growing rhizobia on ethanol. [Bradyrhizobium sp. ; Rhizobium meliloti; Rhizobium loti; Rhizobium leguminosarum; Rhizobium fredii; Bradyrhizobium japonicum

    SciTech Connect

    Sadowsky, M.J.; Bohlool, B.B.

    1986-10-01

    Free-living soybean rhizobia and Bradyrhizobium spp. (lupine) have the ability to catabolize ethanol. Of the 30 strains of rhizobia examined, only the fast- and slow-growing soybean rhizobia and the slow-growing Bradyrhizobium sp (lupine) were capable of using ethanol as a sole source of carbon and energy for growth. Two strains from each of the other Rhizobium species examined (R. meliloti, R. loti, and R. leguminosarum biovars phaseoli, trifolii, and viceae) failed to grow on ethanol. One Rhizobium fredii (fast-growing) strain, USDA 191, and one (slow-growing) Bradyrhizobium japonicum strain, USDA 110, grew in ethanol up to concentrations of 3.0 and 1.0%, respectively. While three of the R. fredii strains examined (USDA 192, USDA 194, and USDA 205) utilized 0.2% acetate, only USDA 192 utilized 0.1% n-propanol. None of the three strains utilized 0.1% methanol, formate, or n-butanol as the sole carbon source.

  20. Identification of Rhizobium-specific intergenic mosaic elements within an essential two-component regulatory system of Rhizobium species.

    PubMed Central

    Osterås, M; Stanley, J; Finan, T M

    1995-01-01

    Analysis of the DNA regions upstream of the phosphoenolpyruvate carboxykinase gene (pckA) in Rhizobium meliloti and Rhizobium sp. strain NGR234 identified an open reading frame which was highly homologous to the Agrobacterium tumefaciens chromosomal virulence gene product ChvI. A second gene product, 500 bp downstream of the chvI-like gene in R. meliloti, was homologous to the A. tumefaciens ChvG protein. The homology between the R. meliloti and A. tumefaciens genes was confirmed, because the R. meliloti chvI and chvG genes complemented A. tumefaciens chvI and chvG mutants for growth on complex media. We were unable to construct chvI or chvG insertion mutants of R. meliloti, whereas mutants carrying insertions outside of these genes were readily obtained. A 108-bp repeat element characterized by two large palindromes was identified in the chvI and chvG intergenic regions of both Rhizobium species. This element was duplicated in Rhizobium sp. strain NGR234. Another structurally similar element with a size of 109 bp was present in R. meliloti but not in Rhizobium sp. strain NGR234. These elements were named rhizobium-specific intergenic mosaic elements (RIMEs), because their distribution seems to be limited to members of the family Rhizobiaceae. A homology search in GenBank detected six more copies of the first element (RIME1), all in Rhizobium species, and three extra copies of the second element (RIME2), only in R. meliloti. Southern blot analysis with a probe specific to RIME1 showed the presence of several copies of the element in the genome of R. meliloti, Rhizobium sp. strain NGR234, Rhizobium leguminosarum, and Agrobacterium rhizogenes, but none was present in A. tumefaciens and Bradyrhizobium japonicum. PMID:7559334

  1. Studying Plant-Rhizobium Mutualism in the Biology Classroom: Connecting the Big Ideas in Biology through Inquiry

    ERIC Educational Resources Information Center

    Suwa, Tomomi; Williamson, Brad

    2014-01-01

    We present a guided-inquiry biology lesson, using the plant-rhizobium symbiosis as a model system. This system provides a rich environment for developing connections between the big ideas in biology as outlined in the College Board's new AP Biology Curriculum. Students gain experience with the practice of scientific investigation, from…

  2. Uptake and Metabolism of Carbohydrates by Bradyrhizobium japonicum Bacteroids 1

    PubMed Central

    Salminen, Seppo O.; Streeter, John G.

    1987-01-01

    Bradyrhizobium japonicum bacteroids were isolated anaerobically and were supplied with 14C-labeled trehalose, sucrose, UDP-glucose, glucose, or fructose under low O2 (2% in the gas phase). Uptake and conversion of 14C to CO2 were measured at intervals up to 90 minutes. Of the five compounds studied, UDP-glucose was most rapidly absorbed but it was very slowly metabolized. Trehalose was the sugar most rapidly converted to CO2, and fructose was respired at a rate at least double that of glucose. Sucrose and glucose were converted to CO2 at a very low but measurable rate (<0.1 nanomoles per milligram protein per hour). Carbon Number 1 of glucose appeared in CO2 at a rate 30 times greater than the conversion of carbon Number 6 to CO2, indicating high activity of the pentose phosphate pathway. Enzymes of the Entner-Doudoroff pathway were not detected in bacteroids, but very low activities of sucrose synthase and phosphofructokinase were demonstrated. Although metabolism of sugars by B. japonicum bacteroids was clearly demonstrated, the rate of sugar uptake was only 1/30 to 1/50 the rate of succinate uptake. The overall results support the view that, although bacteroids metabolize sugars, the rates are very low and are inadequate to support nitrogenase. PMID:16665284

  3. Transposon mutagenesis of Bacteroides fragilis using a mariner transposon vector.

    PubMed

    Veeranagouda, Yaligara; Husain, Fasahath; Wexler, Hannah M

    2013-08-01

    The mariner transposon vector pYV07 was tested for use in the mutagenesis of Bacteroides fragilis 638R. The transposon vector efficiently generated mutants in B. fragilis 638R. The transposon disrupted genes were scattered throughout the genome of B. fragilis 638R. This method serves as a powerful tool to study B. fragilis. PMID:23664906

  4. Differential Decay of Human Faecal Bacteroides in Marine and Freshwater

    EPA Science Inventory

    Gene sequences from Bacteroides and relatives are being considered for the enumeration of aquatic fecal contamination and estimation of public health risk. To interpret these data, it is necessary to understand the decay of molecular and cultivated indicators and pathogens in en...

  5. Bacteroides: the Good, the Bad, and the Nitty-Gritty

    PubMed Central

    Wexler, Hannah M.

    2007-01-01

    Summary: Bacteroides species are significant clinical pathogens and are found in most anaerobic infections, with an associated mortality of more than 19%. The bacteria maintain a complex and generally beneficial relationship with the host when retained in the gut, but when they escape this environment they can cause significant pathology, including bacteremia and abscess formation in multiple body sites. Genomic and proteomic analyses have vastly added to our understanding of the manner in which Bacteroides species adapt to, and thrive in, the human gut. A few examples are (i) complex systems to sense and adapt to nutrient availability, (ii) multiple pump systems to expel toxic substances, and (iii) the ability to influence the host immune system so that it controls other (competing) pathogens. B. fragilis, which accounts for only 0.5% of the human colonic flora, is the most commonly isolated anaerobic pathogen due, in part, to its potent virulence factors. Species of the genus Bacteroides have the most antibiotic resistance mechanisms and the highest resistance rates of all anaerobic pathogens. Clinically, Bacteroides species have exhibited increasing resistance to many antibiotics, including cefoxitin, clindamycin, metronidazole, carbapenems, and fluoroquinolones (e.g., gatifloxacin, levofloxacin, and moxifloxacin). PMID:17934076

  6. Effects of nano-TiO₂ on the agronomically-relevant Rhizobium-legume symbiosis.

    PubMed

    Fan, Ruimei; Huang, Yu Chu; Grusak, Michael A; Huang, C P; Sherrier, D Janine

    2014-01-01

    The impact of nano-TiO₂ on Rhizobium-legume symbiosis was studied using garden peas and the compatible bacterial partner Rhizobium leguminosarum bv. viciae 3841. Exposure to nano-TiO₂ did not affect the germination of peas grown aseptically, nor did it impact the gross root structure. However, nano-TiO₂ exposure did impact plant development by decreasing the number of secondary lateral roots. Cultured R. leguminosarum bv. viciae 3841 was also impacted by exposure to nano-TiO₂, resulting in morphological changes to the bacterial cells. Moreover, the interaction between these two organisms was disrupted by nano-TiO₂ exposure, such that root nodule development and the subsequent onset of nitrogen fixation were delayed. Further, the polysaccharide composition of the walls of infected cells of nodules was altered, suggesting that the exposure induced a systemic response in host plants. Therefore, nano-TiO₂ contamination in the environment is potentially hazardous to the Rhizobium-legume symbiosis system. PMID:23933452

  7. RNA-Seq and Microarrays Analyses Reveal Global Differential Transcriptomes of Mesorhizobium huakuii 7653R between Bacteroids and Free-Living Cells

    PubMed Central

    Peng, Jieli; Hao, Baohai; Liu, Liu; Wang, Shanming; Ma, Binguang; Yang, Yi; Xie, Fuli; Li, Youguo

    2014-01-01

    Mesorhizobium huakuii 7653R occurs either in nitrogen-fixing symbiosis with its host plant, Astragalus sinicus, or free-living in the soil. The M. huakuii 7653R genome has recently been sequenced. To better understand the complex biochemical and developmental changes that occur in 7653R during bacteroid development, RNA-Seq and Microarrays were used to investigate the differential transcriptomes of 7653R bacteroids and free-living cells. The two approaches identified several thousand differentially expressed genes. The most prominent up-regulation occurred in the symbiosis plasmids, meanwhile gene expression is concentrated to a set of genes (clusters) in bacteroids to fulfill corresponding functional requirements. The results suggested that the main energy metabolism is active while fatty acid metabolism is inactive in bacteroid and that most of genes relevant to cell cycle are down-regulated accordingly. For a global analysis, we reconstructed a protein-protein interaction (PPI) network for 7653R and integrated gene expression data into the network using Cytoscape. A highly inter-connected subnetwork, with function enrichment for nitrogen fixation, was found, and a set of hubs and previously uncharacterized genes participating in nitrogen fixation were identified. The results described here provide a broader biological landscape and novel insights that elucidate rhizobial bacteroid differentiation, nitrogen fixation and related novel gene functions. PMID:24695521

  8. Optimization of Dairy Sludge for Growth of Rhizobium Cells

    PubMed Central

    Singh, Ashok Kumar; Singh, Gauri; Gautam, Digvijay; Bedi, Manjinder Kaur

    2013-01-01

    In this study dairy sludge was evaluated as an alternative cultivation medium for Rhizobium. Growth of bacterial strains at different concentrations of Dairy sludge was monitored. Maximum growth of all strains was observed at 60% Dairy sludge concentration. At 60% optical density (OD) values are 0.804 for Rhizobium trifolii (MTCC905), 0.825 for Rhizobium trifolii (MTCC906), and 0.793 for Rhizobium meliloti (MTCC100). Growth pattern of strains was observed at 60% Dairy sludge along with different synthetic media (tryptone yeast, Rhizobium minimal medium and yeast extract mannitol). Growth in 60% Dairy sludge was found to be superior to standard media used for Rhizobium. Media were optimized using 60% dairy sludge along with different concentrations of yeast extract (1–7 g/L) and mannitol (7–13 g/L) in terms of optical density at different time intervals, that is, 24, 48 and 72 hours. Maximum growth was observed in 6 g/L of yeast extract and 12 g/L of mannitol at 48-hour incubation period in all strains. The important environmental parameters such as pH were optimized using 60% dairy sludge, 60% dairy sludge +6 g/L yeast extract, and 60% dairy sludge +12 g/L mannitol. The maximum growth of all strains was found at pH 7.0. The present study recommends the use of 60% dairy sludge as a suitable growth medum for inoculant production. PMID:24089690

  9. Detection of Bacteroides fragilis Enterotoxin Gene by PCR

    PubMed Central

    Shetab, Razeq; Cohen, Stuart H.; Prindiville, Thomas; Tang, Yajarayma J.; Cantrell, Mary; Rahmani, Darush; Silva, Joseph

    1998-01-01

    Bacteroides fragilis constitutes about 1% of the bacterial flora in intestines of normal humans. Enterotoxigenic strains of B. fragilis have been associated with diarrheal diseases in humans and animals. The enterotoxin produced by these isolates induces fluid changes in ligated intestinal loops and an in vitro cytotoxic response in HT-29 cells. We developed a nested PCR to detect the enterotoxin gene of B. fragilis in stool specimens. After DNA extraction, a 367-bp fragment was amplified with two outer primers. The amplicon from this reaction was subjected to a second round of amplification with a set of internal primers. With these inner primers, a 290-bp DNA fragment was obtained which was confirmed as part of the B. fragilis enterotoxin gene by Southern blotting with a nonradioactive internal probe and a chemiluminescence system. By this approach, B. fragilis enterotoxin gene sequences were detected in eight known enterotoxigenic human isolates and nine enterotoxigenic horse isolates. No amplification products were obtained from DNA extracted from 28 nonenterotoxigenic B. fragilis isolates or B. distasonis, B. thetaiotaomicron, B. uniformis, B. ovatus, Escherichia coli, or Clostridium difficile. The sensitivity of this assay allowed us to detect as little as 1 pg of enterotoxin DNA sequences or 100 to 1,000 cells of enterotoxigenic B. fragilis/g of stool. Enterotoxin production of all isolates was confirmed in vitro in HT-29 cells. A 100% correlation was obtained between enterotoxin detection by cytotoxin assay and the nested PCR assay. This rapid and sensitive assay can be used to identify enterotoxigenic B. fragilis and may be used clinically to determine the role of B. fragilis in diarrheal diseases. PMID:9620408

  10. Rhizobium japonicum USDA 191 has two nodD genes that differ in primary structure and function.

    PubMed

    Appelbaum, E R; Thompson, D V; Idler, K; Chartrain, N

    1988-01-01

    Several Rhizobium genes (designated nod genes) are involved in early steps in nodule formation. Here we present the results of DNA sequence and functional analysis of two nodD genes from the symbiotic plasmid of USDA 191, a fast-growing strain that forms nitrogen-fixing nodules on soybeans. Both genes encoded full-length nodD-related polypeptides, which were 69% homologous to each other. One of these genes, nodD1, complemented a Rhizobium trifolii nodD::Tn5 mutant for clover nodulation; the other gene, nodD2, did not. The nodD1 coding region was preceded by a conserved DNA sequence previously noted in other rhizobia, but no such sequence was found in front of nodD2. Plants inoculated with a nodD1 insertion mutant appeared to be nitrogen starved and had a greatly reduced nodule number. Plants inoculated with a nodD2 mutant had a partially nitrogen-starved appearance and normal nodule number, were slightly delayed in nodule formation, and formed nodules that contained reduced levels of nodulin-35 and had fewer bacteroids per infected plant cell. Thus, both of these genes are involved in symbiosis. USDA 191 carrying extra copies of nodD2 on a plasmid vector had an altered colony morphology that suggested inhibition of exopolysaccharide synthesis. The predicted gene products of nodD1 and nodD2 both showed homology to LysR, an E. coli regulatory protein. We conclude that nodD1 probably has the same function as nodD in temperate rhizobia, namely, activation of nodABC transcription in the presence of plant signals. nodD2 may be involved in regulation of exopolysaccharide synthetic genes. PMID:2826389

  11. Rhizobium leguminosarum bv. viciae 3841 Adapts to 2,4-Dichlorophenoxyacetic Acid with “Auxin-Like” Morphological Changes, Cell Envelope Remodeling and Upregulation of Central Metabolic Pathways

    PubMed Central

    Bhat, Supriya V.; Booth, Sean C.; McGrath, Seamus G. K.; Dahms, Tanya E. S.

    2015-01-01

    There is a growing need to characterize the effects of environmental stressors at the molecular level on model organisms with the ever increasing number and variety of anthropogenic chemical pollutants. The herbicide 2,4-dichlorophenoxyacetic acid (2,4-D), as one of the most widely applied pesticides in the world, is one such example. This herbicide is known to have non-targeted undesirable effects on humans, animals and soil microbes, but specific molecular targets at sublethal levels are unknown. In this study, we have used Rhizobium leguminosarum bv. viciae 3841 (Rlv) as a nitrogen fixing, beneficial model soil organism to characterize the effects of 2,4-D. Using metabolomics and advanced microscopy we determined specific target pathways in the Rlv metabolic network and consequent changes to its phenotype, surface ultrastructure, and physical properties during sublethal 2,4-D exposure. Auxin and 2,4-D, its structural analogue, showed common morphological changes in vitro which were similar to bacteroids isolated from plant nodules, implying that these changes are related to bacteroid differentiation required for nitrogen fixation. Rlv showed remarkable adaptation capabilities in response to the herbicide, with changes to integral pathways of cellular metabolism and the potential to assimilate 2,4-D with consequent changes to its physical and structural properties. This study identifies biomarkers of 2,4-D in Rlv and offers valuable insights into the mode-of-action of 2,4-D in soil bacteria. PMID:25919284

  12. Average nucleotide identity of genome sequences supports the description of Rhizobium lentis sp. nov., Rhizobium bangladeshense sp. nov. and Rhizobium binae sp. nov. from lentil (Lens culinaris) nodules.

    PubMed

    Rashid, M Harun-or; Young, J Peter W; Everall, Isobel; Clercx, Pia; Willems, Anne; Santhosh Braun, Markus; Wink, Michael

    2015-09-01

    Rhizobial strains isolated from effective root nodules of field-grown lentil (Lens culinaris) from different parts of Bangladesh were previously analysed using sequences of the 16S rRNA gene, three housekeeping genes (recA, atpD and glnII) and three nodulation genes (nodA, nodC and nodD), DNA fingerprinting and phenotypic characterization. Analysis of housekeeping gene sequences and DNA fingerprints indicated that the strains belonged to three novel clades in the genus Rhizobium. In present study, a representative strain from each clade was further characterized by determination of cellular fatty acid compositions, carbon substrate utilization patterns and DNA-DNA hybridization and average nucleotide identity (ANI) analyses from whole-genome sequences. DNA-DNA hybridization showed 50-62% relatedness to their closest relatives (the type strains of Rhizobium etli and Rhizobium phaseoli) and 50-60% relatedness to each other. These results were further supported by ANI values, based on genome sequencing, which were 87-92% with their close relatives and 88-89% with each other. On the basis of these results, three novel species, Rhizobium lentis sp. nov. (type strain BLR27(T) = LMG 28441(T) = DSM 29286(T)), Rhizobium bangladeshense sp. nov. (type strain BLR175(T) = LMG 28442(T) = DSM 29287(T)) and Rhizobium binae sp. nov. (type strain BLR195(T) = LMG 28443(T) = DSM 29288(T)), are proposed. These species share common nodulation genes (nodA, nodC and nodD) that are similar to those of the symbiovar viciae. PMID:26060217

  13. Rhizobium helianthi sp. nov., isolated from the rhizosphere of sunflower.

    PubMed

    Wei, Xuexin; Yan, Shouwei; Li, Dai; Pang, Huancheng; Li, Yuyi; Zhang, Jianli

    2015-12-01

    A Gram-stain-negative, non-spore-forming, rod-shaped and aerobic bacterium, designated Xi19T, was isolated from a soil sample collected from the rhizosphere of sunflower (Helianthus annuus) in Wuyuan county of Inner Mongolia, China and was characterized taxonomically by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel isolate was related to species of the genus Rhizobium, sharing the greatest 16S rRNA gene sequence similarity with Rhizobium rhizoryzae J3-AN59T (98.4 %), followed by Rhizobium pseudoryzae J3-A127T (97.4 %). There were low similarities ( < 91 %) between the atpD, recA and glnII gene sequences of the novel strain and those of members of the genus Rhizobium. DNA-DNA hybridization values between strain Xi19T and the most related strain Rhizobium rhizoryzae J3-AN59T were low. The major cellular fatty acids of strain Xi19T were C16 : 0, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C19 : 0 cyclo ω8c. Q-10 was identified as the predominant ubiquinone and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The DNA G+C content of strain Xi19T was 60.2 mol%. On the basis of physiological and biochemical characteristics, coupled with genotypic data obtained in this work, strain Xi19T represents a novel species of the genus Rhizobium, for which the name Rhizobium helianthi is proposed. The type strain is Xi19T ( = CGMCC 1.12192T = KCTC 23879T). PMID:26364048

  14. Specificity of a Bacteroides thetaiotaomicron marker for human feces

    USGS Publications Warehouse

    Carson, C.A.; Christiansen, J.M.; Yampara-Iquise, H.; Benson, V.W.; Baffaut, C.; Davis, J.V.; Broz, R.R.; Kurtz, W.B.; Rogers, W.M.; Fales, W.H.

    2005-01-01

    A bacterial primer set, known to produce a 542-bp amplicon specific for Bacteroides thetaiotaomicron, generated this product in PCR with 1 ng of extracted DNA from 92% of 25 human fecal samples, 100% of 20 sewage samples, and 16% of 31 dog fecal samples. The marker was not detected in 1 ng of fecal DNA from 61 cows, 35 horses, 44 pigs, 24 chickens, 29 turkeys, and 17 geese. Copyright ?? 2005, American Society for Microbiology. All Rights Reserved.

  15. Tn4351 transposes in Bacteroides spp. and mediates the integration of plasmid R751 into the Bacteroides chromosome

    SciTech Connect

    Shoemaker, N.B.; Getty, C.; Gardner, J.F.; Salyers, A.A.

    1986-03-01

    The gene for resistance to erythromycin and clindamycin, which is carried on the conjugative Bacteroides plasmid, pBF4, has been shown previously to be part of an element (Tn4351) that transposes in Escherichia coli. The authors have now introduced Tn4351 into Bacteroides uniformis 0061 on the following two suicide vectors: (i) the broad-host-range IncP plasmid R751 (R751::Tn4351) and (ii) pSS-2, a chimeric plasmid which contains 33 kilobases of pBF4 (including Tn4351) cloned into the IncQ plasmid RSF1010 and which is mobilized by R751. When E. coli HB101, carrying either R751::Tn4351 or R751 and pSS-2, was mated with B. uniformis under aerobic conditions, Em/sup r/ transconjugants were detected at a frequency of 10 /sup -6/ to 10/sup -5/ (R751::Tn4351) or 10/sup -8/ to 10/sup -6/ (R751 and pSS-2). In matings involving pSS-2, all Em/sup r/ transconjugants contained simple insertions of Tn4351 in the chromosome, whereas in matings involving R751::Tn4351, about half of the Em/sup r/ transconjugants had R751 cointegrated with Tn4351 in the chromosome. Of the Em/sup r/ transconjugants, 13% were auxotrophs. Bacteroides spp. which had R751 cointegrated with Tn4351 in the chromosome did not transfer R751 or Tn4351 to E. coli HB101 or to isogenic B. uniformis, nor did the integrated R751 mobilize pE5-2, an E. coli-Bacteroides shuttle vector that contains a transfer origin that is recognized by R751.

  16. Nodules are induced on alfalfa roots by Agrobacterium tumefaciens and Rhizobium trifolii containing small segments of the Rhizobium meliloti nodulation region

    SciTech Connect

    Hirsch, A.M.; Drake, D.; Jacobs, T.W.; Long, S.R.

    1985-01-01

    Regions of the Rhizobium meliloti nodulation genes from the symbiotic plasmid were transferred to Agrobacterium tumefaciens and Rhizobium trifolii by conjugation. The A. tumefaciens and R. trifolii trans-conjugants were unable to elicit curling of alfalfa root hairs, but were able to induce nodule development at a low frequency. These were judged to be genuine nodules on the basis of cytological and developmental criteria. Like genuine alfalfa nodules, the nodules were initiated from divisions of the inner root cortical cells. They developed a distally positioned meristem and several peripheral vascular bundles. An endodermis separated the inner tissues of the nodule from the surrounding cortex. No infection threads were found to penetrate either root hairs or the nodule cells. Bacteria were found only in intercellular spaces. Thus, alfalfa nodules induced by A. tumefaciens and R. trifolii transconjugants carrying small nodulation clones of R. meliloti were completely devoid of intracellular bacteria. When these strains were inoculated onto white clover roots, small nodule-like protrusions developed that, when examined cytologically, were found to more closely resemble roots than nodules. Although the meristem was broadened and lacked a root cap, the protrusions had a central vascular bundle and other rootlike features. The results suggest that morphogenesis of alfalfa root nodules can be uncoupled from infection thread formation. The genes encoded in the 8.7-kilobase nodulation fragment are sufficient in A. tumefaciens or R. trifolii backgrounds for nodule morphogenesis.

  17. Survival of Rhizobium inoculum in hydroseeding slurries

    SciTech Connect

    Brown, M.B.; Wolf, D.D.; Morse, R.D.; Neal, J.L.

    1982-12-01

    Disturbed lands such as surface mined areas generally require fertilizer, lime, mulch, and seed for revegetation. Hydroseeding is the most widely used seeding method for mountainous terrain. Where legumes are included in the mixture, Rhizobium inoculum is recommended since disturbed areas are likely to lack indigenous rhizobia. The pH and viability of rhizobia cells in hydroseeder mix slurries were determined in order to establish recommendations for hydroseeding conditions. Of the fertilizer components commonly used for hydroseeding only those containing phosphorus influenced slurry pH. Varying concentrations of triple superphosphate (TSP) and diammonium phosphate (DAP) resulted in hydroseeder mixture pH values ranging from 2.9 to 7.7, respectively. Significant loss of viability of rhizobia occurred at pH values of less than 6.0. In practice, a hydroseeding slurry should contain enough DAP in the fertilizer blend to have a pH of 6.0 or greater which is equivalent to a ratio of DAP to TSP of 4 to 6. Thus, at least 40 of each 100 kg of phosphate should be supplied by DAP. Pulverized agriculture lime did not correct slurry acidity; however, hydrated lime (calcium hydroxide) if added in sufficient amounts could be used to increase the pH to a level that does not significantly alter the viability of the rhizobia.

  18. Characterisation of SalRAB a Salicylic Acid Inducible Positively Regulated Efflux System of Rhizobium leguminosarum bv viciae 3841

    PubMed Central

    Tett, Adrian J.; Karunakaran, Ramakrishnan; Poole, Philip S.

    2014-01-01

    Salicylic acid is an important signalling molecule in plant-microbe defence and symbiosis. We analysed the transcriptional responses of the nitrogen fixing plant symbiont, Rhizobium leguminosarum bv viciae 3841 to salicylic acid. Two MFS-type multicomponent efflux systems were induced in response to salicylic acid, rmrAB and the hitherto undescribed system salRAB. Based on sequence similarity salA and salB encode a membrane fusion and inner membrane protein respectively. salAB are positively regulated by the LysR regulator SalR. Disruption of salA significantly increased the sensitivity of the mutant to salicylic acid, while disruption of rmrA did not. A salA/rmrA double mutation did not have increased sensitivity relative to the salA mutant. Pea plants nodulated by salA or rmrA strains did not have altered nodule number or nitrogen fixation rates, consistent with weak expression of salA in the rhizosphere and in nodule bacteria. However, BLAST analysis revealed seventeen putative efflux systems in Rlv3841 and several of these were highly differentially expressed during rhizosphere colonisation, host infection and bacteroid differentiation. This suggests they have an integral role in symbiosis with host plants. PMID:25133394

  19. Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etli

    PubMed Central

    Resendis-Antonio, Osbaldo; Reed, Jennifer L; Encarnación, Sergio; Collado-Vides, Julio; Palsson, Bernhard Ø

    2007-01-01

    Rhizobiaceas are bacteria that fix nitrogen during symbiosis with plants. This symbiotic relationship is crucial for the nitrogen cycle, and understanding symbiotic mechanisms is a scientific challenge with direct applications in agronomy and plant development. Rhizobium etli is a bacteria which provides legumes with ammonia (among other chemical compounds), thereby stimulating plant growth. A genome-scale approach, integrating the biochemical information available for R. etli, constitutes an important step toward understanding the symbiotic relationship and its possible improvement. In this work we present a genome-scale metabolic reconstruction (iOR363) for R. etli CFN42, which includes 387 metabolic and transport reactions across 26 metabolic pathways. This model was used to analyze the physiological capabilities of R. etli during stages of nitrogen fixation. To study the physiological capacities in silico, an objective function was formulated to simulate symbiotic nitrogen fixation. Flux balance analysis (FBA) was performed, and the predicted active metabolic pathways agreed qualitatively with experimental observations. In addition, predictions for the effects of gene deletions during nitrogen fixation in Rhizobia in silico also agreed with reported experimental data. Overall, we present some evidence supporting that FBA of the reconstructed metabolic network for R. etli provides results that are in agreement with physiological observations. Thus, as for other organisms, the reconstructed genome-scale metabolic network provides an important framework which allows us to compare model predictions with experimental measurements and eventually generate hypotheses on ways to improve nitrogen fixation. PMID:17922569

  20. Rhizobium petrolearium sp. nov., isolated from oil-contaminated soil.

    PubMed

    Zhang, Xiaoxia; Li, Baoming; Wang, Haisheng; Sui, Xinhua; Ma, Xiaotong; Hong, Qing; Jiang, Ruibo

    2012-08-01

    Two Gram-negative, aerobic, rod-shaped bacteria, designated strains SL-1(T) and F11, which had the ability to decompose polycyclic aromatic hydrocarbons (PAHs), were isolated from soil samples contaminated by oil. The cells were motile by polar or lateral flagella. According to comparison of 16S rRNA gene sequences, strains SL-1(T) and F11 were identical and showed the greatest degree of similarity (96.8%) to both Rhizobium oryzae Alt505(T) and Rhizobium mesosinicum CCBAU 25010(T); however, only Rhizobium oryzae with SL-1(T) and F11 formed a separate clade. There were low similarities (<90%) between the atpD and recA sequences of the two strains and those of the genus of Rhizobium. The bacteria grew at temperatures of 10-40 °C with an optimum of 30 °C. The pH range for growth was 6.0-10.0 and optimum pH was 7.0-8.0. Growth occurred at NaCl concentrations up to 3.0% (w/v). They were catalase- and oxidase-positive. The main cellular fatty acids were summed feature 8 (18:1ω7c and/or 18:1ω6c) and 16:0. The DNA G+C content was 62.2 mol%. Strain SL-1(T) showed 29 and 0% DNA-DNA relatedness, respectively, with the most related strains R. oryzae Alt505(T) and R. mesosinicum CCBAU 25010(T) according to phylogenic analysis of the 16S rRNA gene. According to physiological and biochemical characteristics and genotypic data obtained in this work, the bacteria represent a novel species of the genus Rhizobium, and the name Rhizobium petrolearium is proposed. The type strain is SL-1(T) ( = ACCC 11238(T) = KCTC 23288(T)) and it could nodulate Medicago sativa in nodulation tests. PMID:21984664

  1. Rhizobium sophorae sp. nov. and Rhizobium sophoriradicis sp. nov., nitrogen-fixing rhizobial symbionts of the medicinal legume Sophora flavescens.

    PubMed

    Jiao, Yin Shan; Yan, Hui; Ji, Zhao Jun; Liu, Yuan Hui; Sui, Xin Hua; Wang, En Tao; Guo, Bao Lin; Chen, Wen Xin; Chen, Wen Feng

    2015-02-01

    Five bacterial strains representing 45 isolates originated from root nodules of the medicinal legume Sophora flavescens were defined as two novel groups in the genus Rhizobium based on their phylogenetic relationships estimated from 16S rRNA genes and the housekeeping genes recA, glnII and atpD. These groups were distantly related to Rhizobium leguminosarum USDA 2370(T) (95.6 % similarity for group I) and Rhizobium phaseoli ATCC 14482(T) (93.4 % similarity for group II) in multilocus sequence analysis. In DNA-DNA hybridization experiments, the reference strains CCBAU 03386(T) (group I) and CCBAU 03470(T) (group II) showed levels of relatedness of 17.9-57.8 and 11.0-42.9 %, respectively, with the type strains of related species. Both strains CCBAU 03386(T) and CCBAU 03470(T) contained ubiquinone 10 (Q-10) as the major respiratory quinone and possessed 16 : 0, 18 : 0, 19 : 0 cyclo ω8c, summed feature 8 and summed feature 2 as major fatty acids, but did not contain 20 : 3 ω6,8,12c. Phenotypic features distinguishing both groups from all closely related species of the genus Rhizobium were found. Therefore, two novel species, Rhizobium sophorae sp. nov. for group I (type strain CCBAU 03386(T) = E5(T) = LMG 27901(T) = HAMBI 3615(T)) and Rhizobium sophoriradicis sp. nov. for group II (type strain CCBAU 03470(T) = C-5-1(T) = LMG 27898(T) = HAMBI 3510(T)), are proposed. Both groups were able to nodulate Phaseolus vulgaris and their hosts of origin (Sophora flavescens) effectively and their nodulation gene nodC was phylogenetically located in the symbiovar phaseoli. PMID:25385989

  2. Enterotoxigenic and nontoxigenic Bacteroides fragilis strains isolated in Brazil.

    PubMed

    Miranda, Karla R; Dias, Mariana F; Guimarães, Priscilla L S; Boente, Renata F; Pauer, Heidi; Ramos, Priscila Z; Falcão, Laís S; Ferreira, Eliane de O; Balassiano, Ilana T; Ferreira, Livia Q; Santos-Filho, Joaquim dos; Paula, Geraldo R de; Antunes, Eduardo N F; Avelar, Katia E S; Domingues, Regina M C P

    2008-11-01

    The presence of enterotoxigenic Bacteroides fragilis and nontoxigenic B. fragilis (NTBF) among 109 strains isolated from 1980-2008 in Brazil were investigated by PCR. One strain, representing 0.9% of the total analyzed strains, harbored the bft gene which was identified as bft-1 isoform based on PCR-RFLP and sequencing. Forty-nine strains (44.9%) exhibited the NTBF pattern III which possesses the flanking region required for pathogenicity island acquisition in which the bft gene is codified. These data reinforce the potential of B. fragilis as an emerging enteropathogen in our country. PMID:19057827

  3. Characteristics of Bacteroides isolates from the cecum of conventional mice.

    PubMed Central

    Tannock, G W

    1977-01-01

    Bacteroides isolates from the cecum of conventional mice were characterized and grouped according to their ability to ferment or hydrolyze carbohydrates and other compounds believed to be present in the intestinal ecosystem. The isolates were divided into 11 groups on the basis of the fermentation of glucose, cellobiose, gum arabic and xylan (hemicelluloses), N-acetylglucosamine, and dextrin; the hydrolysis of starch and casein (proteolysis); and the production of indole. Stock cultures of B. fragilis, B. distasonis, B. ovatus, B. vulgatus, and B. ruminicola were characterized in the same way. The strains isolated most frequently from the mouse cecum resembled B. fragilis (except that arabinose was fermented) and B. thetaiotaomicron. PMID:869524

  4. Surface location of a Bacteroides gingivalis glycylprolyl protease.

    PubMed Central

    Grenier, D; McBride, B C

    1989-01-01

    Various immunological methods were used to localize a glycylprolyl protease previously isolated from Bacteroides gingivalis ATCC 33277. The results obtained by enzyme-linked immunosorbent assay, indirect immunofluorescence staining, and indirect immunogold labeling suggest that the glycylprolyl protease is present on the surface of the cell outer membrane and is specific to B. gingivalis strains. The enzyme was removed from the cell envelope by treatment of the whole cells with sodium dodecyl sulfate, Triton X-100, sodium deoxycholate, and proteinase K. Images PMID:2807524

  5. Diversity of Rhizobium leguminosarum from pea fields in Washington State

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rhizobia-mediated biological nitrogen (N) fixation in legumes contributes to yield potential in these crops and also provides residual fertilizer to subsequent cereals. Our objectives were to collect isolates of Rhizobium leguminosarum from several pea fields in Washington, examine genetic diversity...

  6. Infection and nodulation of clover by nonmotile Rhizobium trifolii

    SciTech Connect

    Napoli, C.; Albersheim, P.

    1980-02-01

    Nonmotile mutants of Rhizobium trifolii were isolated to determine whether bacterial motility is required for the infection and nodulation of clover. The nonmotile mutants were screened for their ability to infect and nodulate clover seedlings in Fahraeus glass slide assemblies, plastic growth pouches, and vermiculite-sand-filled clay pots. In each system, the nonmotile mutants were able to infect and nodulate clover.

  7. Transposon Tn5 specifies streptomycin resistance in Rhizobium spp.

    PubMed Central

    Selvaraj, G; Iyer, V N

    1984-01-01

    Transposon Tn5 conferred streptomycin resistance on different strains of Rhizobium meliloti, Rhizobium leguminosarum, and Rhizobium trifolii but not on Escherichia coli. A gene (str) specifying this phenotype has been identified and localized on the physical and genetic map of Tn5. It is transcribed from the promoter of neo, the gene that encodes neomycin phosphotransferase. The str gene is downstream from neo in a single transcriptional unit, as revealed by molecular cloning of different segments of Tn5 and by cloning of the neo-str region of Tn5 downstream from a lac promoter. Fusion of the SalI-generated rightward segment of Tn5 (devoid of neo) to a part of a tetracycline resistance gene, tet, in a plasmid or downstream from a lac promoter in a plasmid resulted in significant levels of streptomycin resistance in an R. meliloti host, suggesting that the str gene product can function independent of neomycin phosphotransferase. A natural isolate of R. meliloti that does not express Tn5-associated streptomycin resistance has been identified. We have used the str of Tn5 as a genetic marker in Rhizobium spp. PMID:6327612

  8. A rhizobium selenitireducens protein showing selenite reductase activity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Biobarriers remove, via precipitation, the metalloid selenite (SeO3–2) from groundwater; a process that involves the biological reduction of soluble SeO3–2 to insoluble elemental red selenium (Se0). The enzymes associated with this reduction process are poorly understood. In Rhizobium selenitiredu...

  9. Rhizobium paknamense sp. nov., isolated from lesser duckweeds (Lemna aequinoctialis).

    PubMed

    Kittiwongwattana, Chokchai; Thawai, Chitti

    2013-10-01

    A Gram-stain-negative, rod-shaped bacterium was isolated and designated strain L6-8(T) during a study of endophytic bacterial communities in lesser duckweed (Lemna aequinoctialis). Cells of strain L6-8(T) were motile with peritrichous flagella. The analysis of the nearly complete 16S rRNA gene sequence indicated that strain L6-8(T) was phylogenetically related to species of the genus Rhizobium. Its closest relatives were Rhizobium borbori DN316(T) (97.6 %), Rhizobium oryzae Alt 505(T) (97.3 %) and Rhizobium pseudoryzae J3-A127(T) (97.0 %). The sequence similarity analysis of housekeeping genes recA, glnII, atpD and gyrB showed low levels of sequence similarity (<91.5 %) between strain L6-8(T) and other species of the genus Rhizobium with validly published names. The pH range for growth was 4.0-9.0 (optimum 6.0-7.0), and the temperature range for growth was 20-45 °C (optimum 30 °C). Strain L6-8(T) tolerated NaCl up to 2 % (w/v) (optimum 1 % NaCl). The predominant components of cellular fatty acids were C19 : 0 cyclo ω8c (31.32 %), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 25.39 %) and C16 : 0 (12.03 %). The DNA G+C content of strain L6-8(T) was 60.4 mol% (Tm). nodC and nifH were not amplified in strain L6-8(T). DNA-DNA relatedness between strain L6-8(T) and R. borbori DN316(T), R. oryzae Alt505(T) and R. pseudoryzae J3-A127(T) was between 11.2 and 18.3 %. Based on the sequence similarity analyses, phenotypic, biochemical and physiological characteristics and DNA-DNA hybridization, strain L6-8(T) could be readily distinguished from its closest relatives and represents a novel species of the genus Rhizobium, for which the name Rhizobium paknamense sp. nov. is proposed. The type strain is L6-8(T) ( = NBRC 109338(T) = BCC 55142(T)). PMID:23687054

  10. Protein phosphorylation in Bradyrhizobium japonicum bacteroids and cultures.

    PubMed Central

    Karr, D B; Emerich, D W

    1989-01-01

    Protein phosphorylation was demonstrated in Bradyrhizobium japonicum bacteroids in vivo and in cultures in vivo and in vitro. Comparison of in vivo-labeled phosphoproteins of bacteroids and of cultured cells showed differences in both the pattern and intensity of labeling. In cultured cells, comparison of the labeling patterns and intensities of in vivo- and in vitro-labeled phosphoproteins showed a number of similarities; however, several phosphoproteins were found only after one of the two labeling conditions. The labeling intensity was time dependent in both in vivo and in vitro assays and was dependent on the presence of magnesium in in vitro assays. Differences in the rates of phosphorylation and dephosphorylation were noted for a number of proteins. The level of incorporation of 32P into protein was only 2% or less of the total phosphate accumulated during the in vivo labeling period. Several isolation and sample preparation procedures resulted in differences in labeling patterns. Phosphatase inhibitors and several potential metabolic effectors had negligible effects on the phosphorylation pattern. There were no significant changes in the phosphorylation patterns of cells cultured on mannitol, acetate, and succinate, although the intensity of the labeling did vary with the carbon source. Images PMID:2498290

  11. Protein phosphorylation in Bradyrhizobium japonicum bacteroids and cultures

    SciTech Connect

    Karr, D.B.; Emerich, D.W. )

    1989-06-01

    Protein phosphorylation was demonstrated in Bradyrhizobium japonicum bacteroids in vivo and in cultures in vivo and in vitro. Comparison of in vivo-labeled phosphoproteins of bacteroids and of cultured cells showed differences in both the pattern and intensity of labeling. In cultured cells, comparison of the labeling patterns and intensities of in vivo- and in vitro-labeled phosphoproteins showed a number of similarities; however, several phosphoproteins were found only after one of the two labeling conditions. The labeling intensity was time dependent in both in vivo and in vitro assays and was dependent on the presence of magnesium in in vitro assays. Differences in the rates of phosphorylation and dephosphorylation were noted for a number of proteins. The level of incorporation of {sup 32}P into protein was only 2% or less of the total phosphate accumulated during the in vivo labeling period. Several isolation and sample preparation procedures resulted in differences in labeling patterns. Phosphatase inhibitors and several potential metabolic effectors had negligible effects on the phosphorylation pattern. There were no significant changes in the phosphorylation patterns of cells cultured on mannitol, acetate, and succinate, although the intensity of the labeling did vary with the carbon source.

  12. Determinants of nodulation competitiveness in Rhizobium etli. Final report for period September 30, 1996--September 29, 1999

    SciTech Connect

    Handelsman, Jo

    2000-01-04

    Nitrogen is a major limiting nutrient in crop production. Chemical fertilizers, which are used extensively to meet crop nitrogen requirements, contribute to the high energy inputs of modern agriculture and cause human health and environmental problems. Legumes and their bacterial associates have long been used in crop rotations to replenish soil nitrogen, but effective and reliable biological nitrogen fixation for beans is prevented by the lack of nodulation competitiveness of many Rhizobium strains used as inoculants. The result is that the inoculant strains will not occupy the host's nodules and no benefit will be derived from inoculation. Many indigenous soil strains of Rhizobium etli bv. phaseoli, the symbiont of bean, nodulate but fix little or no nitrogen, and therefore the nodulation competitiveness problem is significant for achieving maximum nitrogen benefit from bean crops. This project was directed toward developing an understanding of the basis of nodulation competitiveness.

  13. Survival of Rhizobium in Acid Soils

    PubMed Central

    Lowendorf, Henry S.; Baya, Ana Maria; Alexander, Martin

    1981-01-01

    A Rhizobium strain nodulating cowpeas did not decline in abundance after it was added to sterile soils at pH 6.9 and 4.4, and the numbers fell slowly in nonsterile soils at pH 5.5 and 4.1. A strain of R. phaseoli grew when added to sterile soils at pH 6.7 and 6.9; it maintained large, stable populations in soils of pH 4.4, 5.5, and 6.0, but the numbers fell markedly and then reached a stable population size in sterile soils at pH 4.3 and 4.4. The abundance of R. phaseoli added to nonsterile soils with pH values of 4.3 to 6.7 decreased similarly with time regardless of soil acidity, and the final numbers were less than in the comparable sterile soils. The minimum pH values for the growth of strains of R. meliloti in liquid media ranged from 5.3 to 5.9. Two R. meliloti strains, which differed in acid tolerance for growth in culture, did not differ in numbers or decline when added to sterile soils at pH 4.8, 5.2, and 6.3. The population size of these two strains was reduced after they were introduced into nonsterile soils at pH 4.8, 5.4, and 6.4, and the number of survivors was related to the soil pH. The R. meliloti strain that was more acid sensitive in culture declined more readily in sterile soil at pH 4.6 than did the less sensitive strain, and only the former strain was eliminated from nonsterile soil at pH 4.8; however, the less sensitive strain also survived better in limed soil. The cell density of the two R. meliloti strains was increased in pH 6.4 soil in the presence of growing alfalfa. The decline and elimination of the tolerant, but not the sensitive, strain was delayed in soil at pH 4.6 by roots of growing alfalfa. PMID:16345909

  14. Protection of sheep against experimental footrot by vaccination with pili purified from Bacteroides nodosus.

    PubMed

    Every, D; Skerman, T M

    1982-10-01

    Merino sheep vaccinated with either whole Bacteroides nodosus organisms, a crude surface antigen preparation or highly purified pili (>99% homogeneity) in oil adjuvant, developed significant resistance to artificial footrot infection when compared with unvaccinated control sheep inoculated with saline-in-oil emulsion (Freund;s incomplete adjuvant) alone. The pili-vaccinated sheep generally had higher K-agglutinating antibody titres than sheep vaccinated with whole B. nodosus. These results confirmed the role of B. nodosus pilus protein both as a protective antigen and the K-agglutinogen. Vaccines prepared with Freund;s incomplete adjuvant containing either purified pili, crude pili or B. nodosus whole cells did not produce significantly different injection-site reactions. PMID:16030827

  15. Rhizobium meliloti exopolysaccharide mutants elicit feedback regulation of nodule formation in alfalfa

    SciTech Connect

    Caetano-Anolles, G.; Lagares, A.; Bauer, W.D. )

    1990-02-01

    Nodule formation by wild-type Rhizobium meliloti is strongly suppressed in younger parts of alfalfa (Medicago sativum L.) root systems as a feedback response to development of the first nodules. Mutants of R. meliloti deficient in exopolysaccharide synthesis can induce the formation of organized nodular structures (pseudonodules) on alfalfa roots but are defective in their ability to invade and multiply within host tissues. The formation of empty pseudonodules by exo mutants was found to elicit a feedback suppression of nodule formation similar to that elicited by the wild-type bacteria. Inoculation of an exo mutant onto one side of a split-root system 24 hours before inoculation of the second side with wild-type cells suppressed wild-type nodule formation on the second side in proportion to the extent of pseudonodule formation by the exo mutants. The formation of pseudonodules is thus sufficient to elicit systemic feedback control of nodulation in the host root system: infection thread development and internal proliferation of the bacteria are not required for elicitation of feedback. Pseudonodule formation by the exo mutants was found to be strongly suppressed in split-root systems by prior inoculation on the opposite side with the wild type. Thus, feedback control elicited by the wild-type inhibits Rhizobium-induced redifferentiation of host root cells.

  16. 5S ribosomal ribonucleic acid sequences in Bacteroides and Fusobacterium: evolutionary relationships within these genera and among eubacteria in general

    NASA Technical Reports Server (NTRS)

    Van den Eynde, H.; De Baere, R.; Shah, H. N.; Gharbia, S. E.; Fox, G. E.; Michalik, J.; Van de Peer, Y.; De Wachter, R.

    1989-01-01

    The 5S ribosomal ribonucleic acid (rRNA) sequences were determined for Bacteroides fragilis, Bacteroides thetaiotaomicron, Bacteroides capillosus, Bacteroides veroralis, Porphyromonas gingivalis, Anaerorhabdus furcosus, Fusobacterium nucleatum, Fusobacterium mortiferum, and Fusobacterium varium. A dendrogram constructed by a clustering algorithm from these sequences, which were aligned with all other hitherto known eubacterial 5S rRNA sequences, showed differences as well as similarities with respect to results derived from 16S rRNA analyses. In the 5S rRNA dendrogram, Bacteroides clustered together with Cytophaga and Fusobacterium, as in 16S rRNA analyses. Intraphylum relationships deduced from 5S rRNAs suggested that Bacteroides is specifically related to Cytophaga rather than to Fusobacterium, as was suggested by 16S rRNA analyses. Previous taxonomic considerations concerning the genus Bacteroides, based on biochemical and physiological data, were confirmed by the 5S rRNA sequence analysis.

  17. Carbohydrate, Organic Acid, and Amino Acid Composition of Bacteroids and Cytosol from Soybean Nodules 1

    PubMed Central

    Streeter, John G.

    1987-01-01

    Metabolites in Bradyrhizobium japonicum bacteroids and in Glycine max (L.) Merr. cytosol from root nodules were analyzed using an isolation technique which makes it possible to estimate and correct for changes in concentration which may occur during bacteroid isolation. Bacteroid and cytosol extracts were fractionated on ion-exchange columns and were analyzed for carbohydrate composition using gas-liquid chromatography and for organic acid and amino acid composition using high performance liquid chromatography. Analysis of organic acids in plant tissues as the phenacyl derivatives is reported for the first time and this approach revealed the presence of several unknown organic acids in nodules. The time required for separation of bacteroids and cytosol was varied, and significant change in concentration of individual compounds during the separation of the two fractions was estimated by calculating the regression of concentration on time. When a statistically significant slope was found, the true concentration was estimated by extrapolating the regression line to time zero. Of 78 concentration estimates made, there was a statistically significant (5% level) change in concentration during sample preparation for only five metabolites: glucose, sucrose, and succinate in the cytosol and d-pinitol and serine in bacteroids. On a mass basis, the major compounds in bacteroids were (descending order of concentration): myo-inositol, d-chiro-inositol, α,α-trehalose, sucrose, aspartate, glutamate, d-pinitol, arginine, malonate, and glucose. On a proportional basis (concentration in bacteroid as percent of concentration in bacteroid + cytosol fractions), the major compounds were: α-aminoadipate (94), trehalose (66), lysine (58), and arginine (46). The results indicate that metabolite concentrations in bacteroids can be reliably determined. PMID:16665774

  18. Expression of pili from Bacteroides nodosus in Pseudomonas aeruginosa.

    PubMed Central

    Elleman, T C; Hoyne, P A; Stewart, D J; McKern, N M; Peterson, J E

    1986-01-01

    The pili of Bacteroides nodosus, the causative agent of ovine footrot, constitute the major host-protective immunogen against homologous serotypic challenge. The pilin gene from B. nodosus 198 has been cloned and morphologically expressed as extracellular pili in Pseudomonas aeruginosa by using a plasmid-borne, thermoregulated expression system. B. nodosus pilin could not be detected in cultures of P. aeruginosa grown at 32 degrees C, but after induction at 37 degrees C, B. nodosus pili were expressed on the cell surface of P. aeruginosa to the virtual exclusion of the host cell pili. Pili harvested from induced P. aeruginosa cultures were used to immunize sheep against footrot. The serum agglutinating antibody titers of vaccinated sheep were comparable to those of sheep receiving pili from B. nodosus. Subsequent challenge of the sheep with B. nodosus 198 indicated that the recombinant- DNA-derived pili vaccine and the B. nodosus pili vaccine provided similar levels of protection against footrot. Images PMID:2877967

  19. Basis for the competitiveness of rhizobium japonicum in nodulation of soybean. Final progress report

    SciTech Connect

    Bauer, W.D.; Evans, W.R.

    1984-07-30

    These studies were concerned with the determination of the characteristics of the soybean symbiont R. japonicum that are crucial to the inoculum competitiveness of one strain of the bacterium over other strains with respect to nodule formation. Our work has been focused on the initial infection events, such as attachment, which precede the development of a fully functional nodule because it is these primary events which determine the success or failure of a particular rhizobia to initiate infections. Experiments concerned with the attachment of R. japonicum to soybean roots have indicated that both soybean symbiotic and non-symbiotic species of rhizobia attach comparably well to soybean roots. There was no evidence of attachment mediated by soybean lectin, as previously claimed, but evidence was obtained for attachment mediated by pili on the Rhizobium cells. It was also found that the efficiency of infection varied substantially with culture age for certain strains while with other strains the efficiency of infection remained approximately constant during growth. We have utilized these observations to investigate the relationship between the efficiency of infection and competitiveness. An unexpected outcome of these studies was the finding that R. japonicum, and other slow-growing Rhizobium species, maintain both viability and symbiotic infectivity over prolonged periods of storage at ambient temperatures when suspended in water. The simplicity and cost-effectiveness of this storage procedure may provide an alternative method to the current practices employed in inoculum preparation. 2 figures, 3 tables.

  20. Genome sequence of the clover symbiont Rhizobium leguminosarum bv. trifolii strain CC275e.

    PubMed

    Delestre, Clément; Laugraud, Aurélie; Ridgway, Hayley; Ronson, Clive; O'Callaghan, Maureen; Barrett, Brent; Ballard, Ross; Griffiths, Andrew; Young, Sandra; Blond, Celine; Gerard, Emily; Wakelin, Steve

    2015-01-01

    Rhizobium leguminosarum bv. trifolii strain CC275e is a highly effective, N2-fixing microsymbiont of white clover (Trifolium repens L.). The bacterium has been widely used in both Australia and New Zealand as a clover seed inoculant and, as such, has delivered the equivalent of millions of dollars of nitrogen into these pastoral systems. R. leguminosarum strain CC275e is a rod-shaped, motile, Gram-negative, non-spore forming bacterium. The genome was sequenced on an Illumina MiSeq instrument using a 2 × 150 bp paired end library and assembled into 29 scaffolds. The genome size is 7,077,367 nucleotides, with a GC content of 60.9 %. The final, high-quality draft genome contains 6693 protein coding genes, close to 85 % of which were assigned to COG categories. This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession JRXL00000000. The sequencing of this genome will enable identification of genetic traits associated with host compatibility and high N2 fixation characteristics in Rhizobium leguminosarum. The sequence will also be useful for development of strain-specific markers to assess factors associated with environmental fitness, competiveness for host nodule occupancy, and survival on legume seeds (New Zealand Ministry of Business, Innovation and Employment program, 'Improving forage legume-rhizobia performance' contract C10X1308 and DairyNZ Ltd.). PMID:26649149

  1. Persistence of Bacteroides ovatus under simulated sunlight irradiation

    PubMed Central

    2014-01-01

    Background Bacteroides ovatus, a member of the genus Bacteroides, is considered for use in molecular-based methods as a general fecal indicator. However, knowledge on its fate and persistence after a fecal contamination event remains limited. In this study, the persistence of B. ovatus was evaluated under simulated sunlight exposure and in conditions similar to freshwater and seawater. By combining propidium monoazide (PMA) treatment and quantitative polymerase chain reaction (qPCR) detection, the decay rates of B. ovatus were determined in the presence and absence of exogenous photosensitizers and in salinity up to 39.5 parts per thousand at 27°C. Results UVB was found to be important for B. ovatus decay, averaging a 4 log10 of decay over 6 h of exposure without the presence of extracellular photosensitizers. The addition of NaNO2, an exogenous sensitizer producing hydroxyl radicals, did not significantly change the decay rate of B. ovatus in both low and high salinity water, while the exogenous sensitizer algae organic matter (AOM) slowed down the decay of B. ovatus in low salinity water. At seawater salinity, the decay rate of B. ovatus was slower than that in low salinity water, except when both NaNO2 and AOM were present. Conclusion The results of laboratory experiments suggest that if B. ovatus is released into either freshwater or seawater environment in the evening, 50% of it may be intact by the next morning; if it is released at noon, only 50% may be intact after a mere 5 min of full spectrum irradiation on a clear day. This study provides a mechanistic understanding to some of the important environmental relevant factors that influenced the inactivation kinetics of B. ovatus in the presence of sunlight irradiation, and would facilitate the use of B. ovatus to indicate the occurrence of fecal contamination. PMID:24993443

  2. Impact of heavy metals on an arctic rhizobium

    SciTech Connect

    Appanna, V.D. )

    1991-03-01

    Bacteria belonging to the genus Rhizobium, when residing in the root nodules of leguminous plants, fix nitrogen and thus contribute very significantly to the global nitrogen and thus contribute very significantly to the global nitrogen budget. Although there is paucity of data concerning the effects of metal pollutants on these agronomically important organisms, their negative impact on the nitrogen fixing ability of these microbes is evident. As rhizobia from root nodules of arctic legumes have been demonstrated to contribute significantly to the ecological balance in this region, the impact of some metals, found in elevated amounts in acidic surroundings on this unique Rhizobium has been assessed. In this paper the ability of the microbe to tolerate abnormal levels of manganese and aluminum is reported and the effectiveness of iron in reversing cadmium toxicity is also discussed.

  3. Regulation of phenolic catabolism in Rhizobium leguminosarum biovar trifolii

    SciTech Connect

    Parke, D. ); Rynne, F.; Glenn, A. )

    1991-09-01

    In members of the family Rhizobiaceae, many phenolic compounds are degraded by the protocatechuate branch of the {beta}-ketoadipate pathway, In this paper the authors describe a novel pattern of induction of protocatechuate (pca) genes in Rhizobium leguminosarum biovar trifolii. Isolation of pca mutant strains revealed that 4-hydroxybenzoate, quinate, and 4-coumarate are degraded via the protocatechuate pathway. At least three inducers govern catabolism of 4-hydroxybenzoate to succinyl coenzyme A and acetyl coenzyme A. The enzyme that catalyzes the initial step is induced by its substrate, whereas the catabolite {beta}-carboxy-cis, cis-muconate induces enzymes for the upper protocatechuate pathway, and {beta}-ketoadipate elicits expression of the enzyme for a subsequent step, {beta}-ketoadipate succinyl-coenzyme A transferase. Elucidation of the induction pattern relied in part on complementation of mutant Rhizobium strains by known subclones of Acinetobacter genes expressed off the lac promoter in a broad-host-range vector.

  4. Rhizobium pongamiae sp. nov. from Root Nodules of Pongamia pinnata

    PubMed Central

    Kesari, Vigya; Ramesh, Aadi Moolam; Rangan, Latha

    2013-01-01

    Pongamia pinnata has an added advantage of N2-fixing ability and tolerance to stress conditions as compared with other biodiesel crops. It harbours “rhizobia” as an endophytic bacterial community on its root nodules. A gram-negative, nonmotile, fast-growing, rod-shaped, bacterial strain VKLR-01T was isolated from root nodules of Pongamia that grew optimal at 28°C, pH 7.0 in presence of 2% NaCl. Isolate VKLR-01 exhibits higher tolerance to the prevailing adverse conditions, for example, salt stress, elevated temperatures and alkalinity. Strain VKLR-01T has the major cellular fatty acid as C18:1  ω7c (65.92%). Strain VKLR-01T was found to be a nitrogen fixer using the acetylene reduction assay and PCR detection of a nifH gene. On the basis of phenotypic, phylogenetic distinctiveness and molecular data (16S rRNA, recA, and atpD gene sequences, G + C content, DNA-DNA hybridization etc.), strain VKLR-01T = (MTCC 10513T = MSCL 1015T) is considered to represent a novel species of the genus Rhizobium for which the name Rhizobium pongamiae sp. nov. is proposed. Rhizobium pongamiae may possess specific traits that can be transferred to other rhizobia through biotechnological tools and can be directly used as inoculants for reclamation of wasteland; hence, they are very important from both economic and environmental prospects. PMID:24078904

  5. Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC 139T)

    SciTech Connect

    Land, Miriam L; Held, Brittany; Gronow, Sabine; Abt, Birte; Lucas, Susan; Glavina Del Rio, Tijana; Nolan, Matt; Tice, Hope; Cheng, Jan-Fang; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, N; Mavromatis, K; Pati, Amrita; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne A.; Chen, Amy; Palaniappan, Krishna; Hauser, Loren John; Brambilla, Evelyne-Marie; Rohde, Manfred; Goker, Markus; Detter, J. Chris; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Lapidus, Alla L.

    2011-01-01

    Bacteroides coprosuis Whitehead et al. 2005 belongs to the genus Bacteroides, which is a member of the family Bacteroidaceae. Members of the genus Bacteroides in general are known as beneficial protectors of animal guts against pathogenic microorganisms, and as contributors to the degradation of complex molecules such as polysaccharides. B. coprosuis itself was isolated from a manure storage pit of a swine facility, but has not yet been found in an animal host. The species is of interest solely because of its isolated phylogenetic location. The genome of B. coprosuis is already the 5th sequenced type strain genome from the genus Bacteroides. The 2,991,798 bp long genome with its 2,461 protein-coding and 78 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  6. Root Exudates of Various Host Plants of Rhizobium leguminosarum Contain Different Sets of Inducers of Rhizobium Nodulation Genes.

    PubMed

    Zaat, S A; Wijffelman, C A; Mulders, I H; van Brussel, A A; Lugtenberg, B J

    1988-04-01

    Rhizobium promoters involved in the formation of root nodules on leguminous plants are activated by flavonoids in plant root exudate. A series of Rhizobium strains which all contain the inducible Rhizobium leguminosarum nodA promoter fused to the Escherichia coli lacZ gene, and which differ only in the source of the regulatory nodD gene, were recently used to show that the regulatory nodD gene determines which flavonoids are able to activate the nodA promoter (HP Spaink, CA Wijffelman, E Pees, RJH Okker, BJJ Lugtenberg 1987 Nature 328: 337-340). Since these strains therefore are able to discriminate between various flavonoids, they were used to determine whether or not plants that are nodulated by R. leguminosarum produce different inducers. After chromatographic separation of root exudate constituents from Vicia sativa L. subsp. nigra (L.), V. hirsuta (L.) S.F. Gray, Pisum sativum L. cv Rondo, and Trifolium subterraneum L., the fractions were tested with a set of strains containing a nodD gene of R. leguminosarum, R. trifolii, or Rhizobium meliloti, respectively. It appeared that the source of nodD determined whether, and to what extent, the R. leguminosarum nodA promoter was induced. Lack of induction could not be attributed to the presence of inhibitors. Most of the inducers were able to activate the nodA promoter in the presence of one particular nodD gene only. The inducers that were active in the presence of the R. leguminosarum nodD gene were different in each root exudate. PMID:16666070

  7. Rhizobium ipomoeae sp. nov., isolated from a water convolvulus field.

    PubMed

    Sheu, Shih-Yi; Chen, Zih-Han; Young, Chiu-Chung; Chen, Wen-Ming

    2016-04-01

    A bacterial strain, designated shin9-1T, was isolated from a water sample taken from a water convolvulus field in Taiwan and characterized using a polyphasic taxonomical approach. Cells of strain shin9-1T were aerobic, Gram-stain-negative, rod-shaped and surrounded by a thick capsule and formed cream-coloured colonies. Growth occurred at 10-45 °C (optimum, 30 °C), with 0-3.0 % NaCl (optimum, 0.5 %) and at pH 7.0-9.0 (optimum, pH 7.0). Strain shin9-1T did not form nodules on a legume plant, Macroptilium atropurpureum, and the nodulation genes nodA, nodC and the nitrogenase reductase gene nifH were not detected by PCR. Phylogenetic analyses based on 16S rRNA and three housekeeping gene sequences (recA, atpD and rpoB) showed that strain shin9-1T belonged to the genus Rhizobium. Strain shin9-1T had the highest level of 16S rRNA gene sequence similarity with respect to Rhizobium daejeonense L61T (97.6 %). The major fatty acid of strain shin9-1T was C18 : 1ω7c. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, phosphatidylmonomethylethanolamine and several uncharacterized lipids. The DNA G+C content was 58.3 mol%. The DNA-DNA relatedness of strain shin9-1T with respect to recognized species of the genus Rhizobium was less than 70 %. Phenotypic characteristics of the novel strain also differed from those of the most closely related species of the genus Rhizobium. On the basis of the phylogenetic inference and phenotypic data, strain shin9-1T should be classified as a representative of a novel species, for which the name Rhizobium ipomoeae sp. nov. is proposed. The type strain is shin9-1T ( = LMG 27163T = KCTC 32148T). PMID:26739022

  8. Draft Genome Sequence of Rhizobium sp. GHKF11, Isolated from Farmland Soil in Pecan Grove, Texas.

    PubMed

    Iyer, Rupa; Damania, Ashish

    2016-01-01

    Rhizobium sp. GHKF11 is an organophosphate-degrading bacterial strain that was isolated from farmland soil in Pecan Grove, Texas, USA. In addition to a capacity for pesticide degradation, GHKF11 shares conserved traits with other Rhizobium spp., including heavy metal resistance and transport genes that may have significant agricultural biotechnology applications. PMID:27445376

  9. Effects of nano-ZnO on the agronomically relevant Rhizobium-legume symbiosis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The impact of nano-ZnO (nZnO) on Rhizobium-legume symbiosis was studied with garden pea and its compatible bacterial partner Rhizobium leguminosarum bv. viciae 3841. Exposure of peas to nZnO had no impact on germination, but significantly affected root length. Chronic exposure of plant to nZnO impac...

  10. Draft Genome Sequence of Rhizobium sp. GHKF11, Isolated from Farmland Soil in Pecan Grove, Texas

    PubMed Central

    Damania, Ashish

    2016-01-01

    Rhizobium sp. GHKF11 is an organophosphate-degrading bacterial strain that was isolated from farmland soil in Pecan Grove, Texas, USA. In addition to a capacity for pesticide degradation, GHKF11 shares conserved traits with other Rhizobium spp., including heavy metal resistance and transport genes that may have significant agricultural biotechnology applications. PMID:27445376

  11. Effects of nano-TiO2 on the agronomically-relevant Rhizobium-legume symbiosis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The impact of nano-TiO2 on Rhizobium-legume symbiosis was studied using garden peas and the compatible bacterial partner Rhizobium leguminosarum bv. viciae 3841. Exposure to nano-TiO2 did not affect the germination of peas grown aseptically, nor did it impact the gross root structure. However, nano-...

  12. Rhizobium selenireducens sp. nov.: A selenite reducing a-Proteobacteria isolated from a bioreactor

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A Gram-negative, non-pigmented bacterium designated strain B1 was isolated from a laboratory bioreactor that reduced selenate to elemental red selenium (Se0). 16S rRNA gene sequence alignment identified the isolate as a Rhizobium sp. belonging to the Rhizobium clade that includes R. daejeonense, R....

  13. Nickel: A micronutrient element for hydrogen-dependent growth of Rhizobium japonicum and for expression of urease activity in soybean leaves

    PubMed Central

    Klucas, Robert V.; Hanus, F. Joe; Russell, Sterling A.; Evans, Harold J.

    1983-01-01

    Soybean plants and Rhizobium japonicum 122 DES, a hydrogen uptake-positive strain, were cultured in media purified to remove Ni. Supplemental Ni had no significant effect on the dry matter or total N content of plants. However, the addition of Ni to both nitrate-grown and symbiotically grown plants resulted in a 7- to 10-fold increase in urease activity (urea amidohydrolase, EC 3.5.1.5) in leaves and significantly increased the hydrogenase activity (EC 1.18.3.1) in isolated nodule bacteroids. When cultured under chemolithotrophic conditions, free-living R. japonicum required Ni for growth and for the expression of hydrogenase activity. Hydrogenase activity was minimal or not detectable in cells incubated either without Ni or with Ni and chloramphenicol. Ni is required for derepression of hydrogenase activity and apparently protein synthesis is necessary for the participation of Ni in hydrogenase expression. The addition of Cr, V, Sn, and Pb in place of Ni failed to stimulate the activity of hydrogenase in R. japonicum and urease in soybean leaves. The evidence indicates that Ni is an important micronutrient element in the biology of the soybean plant and R. japonicum. PMID:16578770

  14. Sphingolipid synthesis deficiency in a mutant of Bacteroides levii

    SciTech Connect

    Brumleve, B.; Lev, M.

    1986-05-01

    Bacteroides levii, an anaerobic bacterium, synthesizes two sphingolipids; the sphingomyelin analogue, ceramide phosphorylethanolamine (CPE), and also ceramide phosphorylglycerol (CPG). The first enzyme in the sphingolipid pathway, 3-ketodihydro-sphingosine (3KDS) synthase, has been partially purified previously. To study subsequent steps in the pathways, mutants defective in sphingolipid synthesis were derived by ethyl methanesulfonate and nitrosoguanidine mutagenesis. Extracts of the mutant, 1075BB, show synthase activity although the cells do not synthesize CPE or CPG. The mutant differs from the wild type in that: (1) synthase activity was much diminished in the mutant, (2) sphingolipid synthesis does not occur in the mutant as evidenced by the absence of spots at sites where CPE and CPG migrate following two-dimensional thin layer chromatography, (3) incorporation of uniformly-labelled (/sup 14/C)serine carbon or (/sup 14/C)3KDS into sphingolipids was not observed in the mutant, (4) following incubation with (/sup 14/C)3KDS, radioactivity corresponding to dihydrosphingosine (DHS) and ceramide were observed in the mutant; no (/sup 14/C)DHS was detected in the wild type, and (5) enhanced incorporation of (/sup 14/C)serine carbon into two lipids not containing phosphorus was found in the mutant. The authors conclude, therefore, that this mutant, 1075BB, has a metabolic block at the terminal biosynthetic steps of sphingolipid synthesis.

  15. DNA Inversion Regulates Outer Membrane Vesicle Production in Bacteroides fragilis

    PubMed Central

    Nakayama-Imaohji, Haruyuki; Hirota, Katsuhiko; Yamasaki, Hisashi; Yoneda, Saori; Nariya, Hirofumi; Suzuki, Motoo; Secher, Thomas; Miyake, Yoichiro; Oswald, Eric; Hayashi, Tetsuya; Kuwahara, Tomomi

    2016-01-01

    Phase changes in Bacteroides fragilis, a member of the human colonic microbiota, mediate variations in a vast array of cell surface molecules, such as capsular polysaccharides and outer membrane proteins through DNA inversion. The results of the present study show that outer membrane vesicle (OMV) formation in this anaerobe is also controlled by DNA inversions at two distantly localized promoters, IVp-I and IVp-II that are associated with extracellular polysaccharide biosynthesis and the expression of outer membrane proteins. These promoter inversions are mediated by a single tyrosine recombinase encoded by BF2766 (orthologous to tsr19 in strain NCTC9343) in B. fragilis YCH46, which is located near IVp-I. A series of BF2766 mutants were constructed in which the two promoters were locked in different configurations (IVp-I/IVp-II = ON/ON, OFF/OFF, ON/OFF or OFF/ON). ON/ON B. fragilis mutants exhibited hypervesiculating, whereas the other mutants formed only a trace amount of OMVs. The hypervesiculating ON/ON mutants showed higher resistance to treatment with bile, LL-37, and human β-defensin 2. Incubation of wild-type cells with 5% bile increased the population of cells with the ON/ON genotype. These results indicate that B. fragilis regulates the formation of OMVs through DNA inversions at two distantly related promoter regions in response to membrane stress, although the mechanism underlying the interplay between the two regions controlled by the invertible promoters remains unknown. PMID:26859882

  16. Determination of some in vitro growth requirements of Bacteroides nodosus.

    PubMed

    Skerman, T M

    1975-03-01

    Physical and nutritional factors required for growth of Bacteroides nodosus isolates from ovine foot-rot lesions were examined. Simplified anaerobic culture techniques were devised utilizing a fully soluble, autoclavable, liquid medium (TAS) which contained proteose-peptone, yeast and meat extracts and certain other essential compounds required to promote prompt and serially transferrable growth of cultures from small inocula. The latter included Trypticase, arginine, a reducing agent (most suitably thioglycollic acid) and CO2; serine and Mg2+ markedly increased growth yields. Trypticase could not be replaced by a commercial preparation of acid-hydrolysed casein; other forms of hydrolysed protein gave delayed and inconsistent growth. Maximum growth of cultures required concentrations of 0-02 to 0-35 M-arginine, which could not be replaced by glutamic acid, citrulline or ornithine. Exogenous carbohydrate compounds were not required. The temperature range for optimum growth of cultures was 37 to 39 degrees C, and anaerobic culture conditions were essential for growth and the production of B. nodosus organisms of normal morphology. Solidified TAS media for the isolation and maintenance of B. nodosus cultures were also devised. PMID:1133574

  17. In vitro utilization of mucin by Bacteroides fragilis.

    PubMed Central

    Roberton, A M; Stanley, R A

    1982-01-01

    A method for isolating pig colon mucin in a soluble high-molecular-weight form, suitable for addition to bacterial growth media, is described. This preparation was utilized as a sole carbohydrate energy source by two strains of Bacteroides fragilis. The extent of degradation was compared with that of commercial pig gastric mucin by the same strains. Gas-liquid chromatographic analysis of the mucin carbohydrates and gel chromatography of the preparations were carried out before and after in vitro degradation. The mucin carbohydrates were utilized only to a very limited extent, colon mucin being more resistant to degradation than gastric mucin. Both mucins chromatographed at or near the excluded volume on Sepharose 4B, and only in the case of ATCC 25285 grown on gastric mucin was a significant degradation peak detected. If mucins are degraded in vivo by the sequential action of several bacteria, a pure culture in vitro might be expected to degrade mucins to a limited extent only. Techniques previously used to examine mucin utilization by pure cultures may have overlooked limited mucin degradation demonstrated by the methods used in this work. PMID:6174077

  18. Genomic Diversity of Enterotoxigenic Strains of Bacteroides fragilis

    PubMed Central

    Pierce, Jessica V.; Bernstein, Harris D.

    2016-01-01

    Enterotoxigenic (ETBF) strains of Bacteroides fragilis are the subset of strains that secrete a toxin called fragilysin (Bft). Although ETBF strains are known to cause diarrheal disease and have recently been associated with colorectal cancer, they have not been well characterized. By sequencing the complete genome of four ETBF strains, we found that these strains exhibit considerable variation at the genomic level. Only a small number of genes that are located primarily in the Bft pathogenicity island (BFT PAI) and the flanking CTn86 conjugative transposon are conserved in all four strains and a fifth strain whose genome was previously sequenced. Interestingly, phylogenetic analysis strongly suggests that the BFT PAI was acquired by non-toxigenic (NTBF) strains multiple times during the course of evolution. At the phenotypic level, we found that the ETBF strains were less fit than the NTBF strain NCTC 9343 and were susceptible to a growth-inhibitory protein that it produces. The ETBF strains also showed a greater tendency to form biofilms, which may promote tumor formation, than NTBF strains. Although the genomic diversity of ETBF strains raises the possibility that they vary in their pathogenicity, our experimental results also suggest that they share common properties that are conferred by different combinations of non-universal genetic elements. PMID:27348220

  19. Novel oligosaccharide constituents of the cellulase complex of Bacteroides cellulosolvens.

    PubMed

    Gerwig, G J; Kamerling, J P; Vliegenthart, J F; Morag, E; Lamed, R; Bayer, E A

    1992-04-15

    The multiple cellulase-containing protein complex, isolated from the cellulolytic bacterium Bacteroides cellulosolvens, contains oligosaccharides which are O-linked mainly to a 230-kDa subunit. The oligosaccharide chains were liberated by alkaline-borohydride treatment and fractionated as oligosaccharide alditols via gel-permeation chromatography and HPLC. The fractions were investigated by one- and two-dimensional (correlation, homonuclear Hartmann-Hahn, rotating-frame nuclear Overhauser enhancement) 500-MHz 1H-NMR spectroscopy in combination with monosaccharide and methylation analyses and with fast-atom-bombardment mass spectrometry. The following carbohydrate structures could be established: [formula: see text] The results indicate an interesting similarity between the oligosaccharide moieties of the cellulase complex of B. cellulosolvens and of Clostridium thermocellum [Gerwig, G. J., Kamerling, J. P., Vliegenthart, J. F. G., Morag (Morgenstern), E., Lamed, R. & Bayer, E. A. (1991) Eur. J. Biochem. 196, 115-122], having 3, 5 and 6 as common elements. The furanose form of a terminal alpha-D-galactose residue demonstrated an inhibitory effect on the interaction of Griffonia simplicifolia I isolectin B4 with the cellulosome-like entity of B. cellulosolvens. PMID:1572372

  20. Ultrastructure of the Bacteroides nodosus cell envelope layers and surface.

    PubMed Central

    Every, D; Skerman, T M

    1980-01-01

    The surface structure and cell envelope layers of various virulent Bacteroides nodosus strains were examined by light microscopy and by electron microscopy by using negative staining, thin-section, and freeze-fracture-etch techniques. Three surface structures were described: pili and a diffuse material, both of which emerged from one or both poles of the bacteria (depending on the stage of growth and division), and large rodlike structures (usually 30 to 40 nm in diameter) associated with a small proportion of the bacterial population. No capsule was detected. The cell envelope consisted of four layers: a plasma membrane, a peptidoglycan layer, an outer membrane, and an outermost additional layer. The additional layer was composed of subunits, generally hexagonally packed with center-to-center spacing of 6 to 7 nm. The outer membrane and plasma membrane freeze-fractured through their hydrophobic regions revealing four fracture faces with features similar to those of other gram-negative bacteria. However, some unusual features were seen on the fracture faces of the outer membrane: large raised ring structure (11 to 12 nm in diameter) on cw 3 at the poles of the bacteria; complementary pits or ring-shaped depressions on cw 2; and small raised ring structures (7 to 8 nm in diameter) all over cw 2. Images PMID:6154040

  1. Genomic Diversity of Enterotoxigenic Strains of Bacteroides fragilis.

    PubMed

    Pierce, Jessica V; Bernstein, Harris D

    2016-01-01

    Enterotoxigenic (ETBF) strains of Bacteroides fragilis are the subset of strains that secrete a toxin called fragilysin (Bft). Although ETBF strains are known to cause diarrheal disease and have recently been associated with colorectal cancer, they have not been well characterized. By sequencing the complete genome of four ETBF strains, we found that these strains exhibit considerable variation at the genomic level. Only a small number of genes that are located primarily in the Bft pathogenicity island (BFT PAI) and the flanking CTn86 conjugative transposon are conserved in all four strains and a fifth strain whose genome was previously sequenced. Interestingly, phylogenetic analysis strongly suggests that the BFT PAI was acquired by non-toxigenic (NTBF) strains multiple times during the course of evolution. At the phenotypic level, we found that the ETBF strains were less fit than the NTBF strain NCTC 9343 and were susceptible to a growth-inhibitory protein that it produces. The ETBF strains also showed a greater tendency to form biofilms, which may promote tumor formation, than NTBF strains. Although the genomic diversity of ETBF strains raises the possibility that they vary in their pathogenicity, our experimental results also suggest that they share common properties that are conferred by different combinations of non-universal genetic elements. PMID:27348220

  2. Suppurative otitis and ascending meningoencephalitis associated with Bacteroides tectus and Porphyromonas gulae in a captive Parma wallaby (Macropus parma) with toxoplasmosis.

    PubMed

    Giannitti, Federico; Schapira, Andrea; Anderson, Mark; Clothier, Kristin

    2014-09-01

    A 6-year-old female Parma wallaby (Macropus parma) at a zoo in California developed acute ataxia and left-sided circling. Despite intensive care, clinical signs progressed to incoordination and prostration, and the animal was euthanized. At necropsy, the left tympanic cavity was filled with homogeneous suppurative exudate that extended into the cranium expanding the meninges and neuroparenchyma in the lateral and ventral aspect of the caudal ipsilateral brainstem and medulla oblongata. Microscopically, the brainstem showed regional severe suppurative meningoencephalitis with large numbers of neutrophils, fewer macrophages, and lymphocytes admixed with fibrin, necrotic cellular debris, hemorrhage, and mineralization, with numerous intralesional Gram-negative bacilli. Bacteroides spp. and Porphyromonas spp. were isolated on anaerobic culture from the meninges, and the bacteria were further characterized by partial 16S ribosomal RNA gene sequencing as Bacteroides tectus and Porphyromonas gulae. Bacterial aerobic culture from the meninges yielded very low numbers of mixed flora and Proteus spp., which were considered contaminants. Culture of Mycoplasma spp. from middle ear and meninges was negative. Additionally, Toxoplasma gondii cysts were detected by immunohistochemistry in the heart and brain, and anti-Toxoplasma antibodies were detected in serum. The genera Bacteroides and Porphyromonas have been associated with oral disease in marsupials; but not with otitis and meningoencephalitis. The results of the present work highlight the importance of performing anaerobic cultures in the diagnostic investigation of cases of suppurative otitis and meningoencephalitis in macropods. PMID:25057163

  3. Genetic snapshots of the Rhizobium species NGR234 genome

    PubMed Central

    Viprey, Virginie; Rosenthal, André; Broughton, William J; Perret, Xavier

    2000-01-01

    Background: In nitrate-poor soils, many leguminous plants form nitrogen-fixing symbioses with members of the bacterial family Rhizobiaceae. We selected Rhizobium sp. NGR234 for its exceptionally broad host range, which includes more than I 12 genera of legumes. Unlike the genome of Bradyrhizobium japonicum, which is composed of a single 8.7 Mb chromosome, that of NGR234 is partitioned into three replicons: a chromosome of about 3.5 Mb, a megaplasmid of more than 2 Mb (pNGR234b) and pNGR234a, a 536,165 bp plasmid that carries most of the genes required for symbioses with legumes. Symbiotic loci represent only a small portion of all the genes coded by rhizobial genomes, however. To rapidly characterize the two largest replicons of NGR234, the genome of strain ANU265 (a derivative strain cured of pNGR234a) was analyzed by shotgun sequencing. Results: Homology searches of public databases with 2,275 random sequences of strain ANU265 resulted in the identification of 1,130 putative protein-coding sequences, of which 922 (41%) could be classified into functional groups. In contrast to the 18% of insertion-like sequences (ISs) found on the symbiotic plasmid pNGR234a, only 2.2% of the shotgun sequences represent known ISs, suggesting that pNGR234a is enriched in such elements. Hybridization data also indicate that the density of known transposable elements is higher in pNGR234b (the megaplasmid) than on the chromosome. Rhizobium-specific intergenic mosaic elements (RIMEs) were found in 35 shotgun sequences, 6 of which carry RIME2 repeats previously thought to be present only in Rhizobium meliloti. As non-overlapping shotgun sequences together represent approximately 10% of ANU265 genome, the chromosome and megaplasmid may carry a total of over 200 RIMEs. Conclusions: 'Skimming' the genome of Rhizobium sp. NGR234 sheds new light on the fine structure and evolution of its replicons, as well as on the integration of symbiotic functions in the genome of a soil bacterium

  4. Comparative properties of glutamine synthetases I and II in Rhizobium and Agrobacterium spp.

    PubMed Central

    Fuchs, R L; Keister, D L

    1980-01-01

    Some properties of glutamine synthetase I (GSI) and GSII are described for a fast-growing Rhizobium sp. (Rhizobium trifolii T1), a slow-growing Rhizobium sp. (Rhizobium japonicum USDA 83), and Agrobacterium tumefaciens C58. GSII of the fast-growing Rhizobium sp. and GSII of the Agrobacterium sp. were considerably more heat labile than GSII of the slow-growing Rhizobium sp. As previously shown in R. japonicum 61A76, GSI became adenylylated rapidly in all species tested in response to ammonium. GSII activity disappeared within one generation of growth in two of the strains, but the disappearance of GSII activity required two generations in another. Isoactivity points for transferase assay, which were derived from the pH curves of adenylylated GSI and deadenylylated GSI, were approximately pH 7.8 for both R. trifolii and A. tumefaciens. No isoactivity point was found for R. japonicum under the standard assay conditions used. When the feedback inhibitor glycine was used to inhibit differentially the adenylylated GSI and deadenylylated GSI of R. japonicum, an isoactivity point was observed at pH 7.3. Thus, the transferase activity of GSI could be determined independent of the state of adenylation. A survey of 23 strains of bacteria representing 11 genera indicated that only Rhizobium spp. and Agrobacterium spp. contained GSII. Thus, this enzyme appears to be unique for the Rhizobiaceae. PMID:6107288

  5. Fate of Nodule-Specific Polysaccharide Produced by Bradyrhizobium japonicum Bacteroids.

    PubMed

    Streeter, J. G.; Peters, N. K.; Salminen, S. O.; Pladys, D.; Zhaohua, P.

    1995-03-01

    A polysaccharide produced by Bradyrhizobium japonicum bacteroids in nodules (NPS) on soybean (Glycine max [L.] Merr.) roots is different in composition and structure from the extracellular polysaccharide produced in culture by this organism. Isogenic strains either capable or incapable of NPS synthesis supported similar rates of plant growth and nitrogenase activity, indicating that polysaccharide deposition was not detrimental. The possibility that NPS may have some protective or nutritional role for bacteroids was considered. Analysis of disintegrating nodules over periods of 1 to 3 months indicated greater recovery of viable bacteria from NPS+ nodules prior to the breakdown of NPS. During and after the breakdown of NPS, the decline in viable bacteria was similar for NPS+ and NPS- strains. Bacteroid destruction in senescing nodules may be accelerated by exposure to proteolytic enzymes in host cytoplasm; however, highly purified NPS had no significant effect on the in vitro activity of partially purified proteases, so protection of bacteroids via this mechanism is unlikely. B. japonicum USDA 438 did not utilize NPS as a carbon source for growth in liquid culture. In vitro assays of NPS depolymerase activity in cultured bacteria and bacteroids were negative using a variety of strains, all of which contained extracellular polysaccharide depolymerase. It seems highly unlikely that B. japonicum can utilize the polysaccharide it synthesizes in nodules, and NPS breakdown in senescing nodules is probably caused by saprophytic fungi. PMID:12228408

  6. Relative adherence of Bacteroides species and strains to Actinomyces viscosus on saliva-coated hydroxyapatite

    SciTech Connect

    Li, J.; Ellen, R.P. )

    1989-09-01

    The study was designed to compare the adherence of several Bacteroides species to A. viscosus. Using 3H, we labeled 24 laboratory strains, including 13 Bacteroides species and 11 fresh clinical isolates of three Bacteroides species. Their adherence to A. viscosus bound to a saliva-coated mineral surface was quantified by liquid scintillation. Adherence relative to a standard strain, B. gingivalis 2561, was compared. Among the lab bacteroides, those of B. gingivalis (eight strains) were the greatest binders (mean, 80.5 {plus minus} 12.4%). Strains of other lab bacteroides bound less well (mean, 33.4 {plus minus} 6.3%). The difference in means was statistically significant (p less than 0.01). The mean for B. gingivalis strains was also significantly greater than that for strains of B. intermedius (51.7 {plus minus} 6.2%). Attachment of B. gingivalis was saturable in experiments in which either input concentration or time was the independent variable, indicating that B. gingivalis cells do not accumulate in this vitro simulation of plaque formation by binding to each other. Subculture did not seem to affect the degree of binding.

  7. Fate of Nodule-Specific Polysaccharide Produced by Bradyrhizobium japonicum Bacteroids.

    PubMed Central

    Streeter, J. G.; Peters, N. K.; Salminen, S. O.; Pladys, D.; Zhaohua, P.

    1995-01-01

    A polysaccharide produced by Bradyrhizobium japonicum bacteroids in nodules (NPS) on soybean (Glycine max [L.] Merr.) roots is different in composition and structure from the extracellular polysaccharide produced in culture by this organism. Isogenic strains either capable or incapable of NPS synthesis supported similar rates of plant growth and nitrogenase activity, indicating that polysaccharide deposition was not detrimental. The possibility that NPS may have some protective or nutritional role for bacteroids was considered. Analysis of disintegrating nodules over periods of 1 to 3 months indicated greater recovery of viable bacteria from NPS+ nodules prior to the breakdown of NPS. During and after the breakdown of NPS, the decline in viable bacteria was similar for NPS+ and NPS- strains. Bacteroid destruction in senescing nodules may be accelerated by exposure to proteolytic enzymes in host cytoplasm; however, highly purified NPS had no significant effect on the in vitro activity of partially purified proteases, so protection of bacteroids via this mechanism is unlikely. B. japonicum USDA 438 did not utilize NPS as a carbon source for growth in liquid culture. In vitro assays of NPS depolymerase activity in cultured bacteria and bacteroids were negative using a variety of strains, all of which contained extracellular polysaccharide depolymerase. It seems highly unlikely that B. japonicum can utilize the polysaccharide it synthesizes in nodules, and NPS breakdown in senescing nodules is probably caused by saprophytic fungi. PMID:12228408

  8. A Phase-Variable Surface Layer from the Gut Symbiont Bacteroides thetaiotaomicron

    PubMed Central

    Taketani, Mao; Donia, Mohamed S.; Jacobson, Amy N.; Lambris, John D.

    2015-01-01

    ABSTRACT The capsule from Bacteroides, a common gut symbiont, has long been a model system for studying the molecular mechanisms of host-symbiont interactions. The Bacteroides capsule is thought to consist of an array of phase-variable polysaccharides that give rise to subpopulations with distinct cell surface structures. Here, we report the serendipitous discovery of a previously unknown surface structure in Bacteroides thetaiotaomicron: a surface layer composed of a protein of unknown function, BT1927. BT1927, which is expressed in a phase-variable manner by ~1:1,000 cells in a wild-type culture, forms a hexagonally tessellated surface layer. The BT1927-expressing subpopulation is profoundly resistant to complement-mediated killing, due in part to the BT1927-mediated blockade of C3b deposition. Our results show that the Bacteroides surface structure is capable of a far greater degree of structural variation than previously known, and they suggest that structural variation within a Bacteroides species is important for productive gut colonization. PMID:26419879

  9. The enterotoxin of Bacteroides fragilis is a metalloprotease.

    PubMed Central

    Moncrief, J S; Obiso, R; Barroso, L A; Kling, J J; Wright, R L; Van Tassell, R L; Lyerly, D M; Wilkins, T D

    1995-01-01

    During the past decade, strains of Bacteroides fragilis that produce an enterotoxin have been implicated in diarrheal disease in animals and humans. The extracellular enterotoxin has been purified and characterized as a single polypeptide (M(r), approximately 20,000). Single specific primer-PCR was used to clone a portion of the B. fragilis enterotoxin gene. The recombinant protein expressed by the cloned gene fragment reacted with monospecific antibodies to B. fragilis enterotoxin by enzyme-linked immunosorbent assay and immunoblot analysis. The deduced amino acid sequence revealed a signature zinc-binding consensus motif (HEXXHXXGXXH/Met-turn) characteristic of metalloproteases termed metzincins. Sequence comparisons showed close identity to matrix metalloproteases (e.g., human fibroblast collagenase) within the zinc-binding and Met-turn region. Purified enterotoxin contained 1 g-atom of Zn2+ per molecule and hydrolyzed gelatin, azocoll, actin, tropomyosin, and fibrinogen. The enterotoxin also underwent autodigestion. The N-terminal amino acid sequences of two autodigestion products were identical to the deduced amino acid sequence of the recombinant enterotoxin and revealed cleavage at Cys-Leu and Ser-Leu peptide bonds. Gelatinase (type IV collagenase) activity comigrated with the toxin when analyzed by gel fractionation and zymography, indicating that protease activity is due to the enterotoxin and not to a contaminating protease(s). Optimal proteolytic activity occurred at 37 degrees C and pH 6.5. Primary proteolytic cleavage sites in actin were identified, revealing cleavage at Gly-Met and Thr-Leu peptide bonds. Enzymatic activity was inhibited by metal chelators but not by inhibitors of other classes of proteases. Additionally, cytotoxic activity of the enterotoxin on human carcinoma HT-29 cells was inhibited by acetoxymethyl ester EDTA. The metalloprotease activity of the enterotoxin suggests a possible mechanism for enterotoxicity and may have additional

  10. Characterization of an outer membrane mannanase from Bacteroides ovatus.

    PubMed Central

    Gherardini, F C; Salyers, A A

    1987-01-01

    Bacteroides ovatus utilizes guar gum, a high-molecular-weight branched galactomannanan, as a sole source of carbohydrate. No extracellular activity was detectable. Approximately 30% of the total cell-associated mannanase activity partitioned with cell membranes. When inner and outer membranes of B. ovatus were separated on sucrose gradients, the mannanase activity was associated mainly with fractions containing outer membranes. Enzyme activity was solubilized by 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS) or by Triton X-100 at a detergent-to-protein ratio of 1:1. The enzyme was stable for only 4 h at 37 degrees C and for 50 to 60 h at 4 degrees C. Analysis of the products of the CHAPS-solubilized mannanase on Bio-Gel A-5M and Bio-Gel P-10 gel filtration columns indicated that the enzyme breaks guar gum into high-molecular-weight fragments. The CHAPS-solubilized mannanase was partially purified by chromatography on a FPLC Mono Q column. The partially purified mannanase preparation contained three major polypeptides (Mr 94,500, 61,000, and 43,000) and several minor ones. High mannanase activity was seen only when B. ovatus was grown on guar gum. Cross-absorbed antiserum detected two other guar gum-associated outer membrane proteins: a CHAPS-extractable 49,000-dalton polypeptide and a 120,000-dalton polypeptide that was not solubilized by CHAPS. Neither of these polypeptides was detectable in the partially purified mannanase preparation. These results indicate that there are at least two guar gum-associated outer membrane polypeptides other than the mannanase. Images PMID:3553153

  11. NolL of Rhizobium sp. Strain NGR234 Is Required for O-Acetyltransferase Activity

    PubMed Central

    Berck, S.; Perret, X.; Quesada-Vincens, D.; Promé, J.-C.; Broughton, W. J.; Jabbouri, S.

    1999-01-01

    Following (iso)flavonoid induction, nodulation genes of the symbiotic nitrogen-fixing bacterium Rhizobium sp. strain NGR234 elaborate a large family of lipooligosaccharidic Nod factors (NodNGR factors). When secreted into the rhizosphere of compatible legumes, these signal molecules initiate root hair deformation and nodule development. The nonreducing glucosamine residue of NodNGR factors are N acylated, N methylated, and mono- or biscarbamoylated, while position C-6 of the reducing extremity is fucosylated. This fucose residue is normally 2-O methylated and either sulfated or acetylated. Here we present an analysis of all acetylated NodNGR factors, which clearly shows that the acetate group may occupy position C-3 or C-4 of the fucose moiety. Disruption of the flavonoid-inducible nolL gene, which is preceded by a nod box, results in the synthesis of NodNGR factors that lack the 3-O- or 4-O-acetate groups. Interestingly, the nodulation capacity of the mutant NGRΩnolL is not impaired, whereas introduction of the nod box::nolL construct into the related strain Rhizobium fredii USDA257 extends the host range of this bacterium to Calopogonium caeruleum, Leucaena leucocephala, and Lotus halophilus. Nod factors produced by a USDA257(pnolL) transconjugant were also acetylated. The nod box::nolL construct was also introduced into ANU265 (NGR234 cured of its symbiotic plasmid), along with extra copies of the nodD1 gene. When permeabilized, these cells possessed acetyltransferase activity, although crude extracts did not. PMID:9922261

  12. [Infective endocarditis by Rhizobium radiobacter. A case report].

    PubMed

    Piñerúa Gonsálvez, Jean Félix; Zambrano Infantinot, Rosanna del Carmen; Calcaño, Carlos; Montaño, César; Fuenmayor, Zaida; Rodney, Henry; Rodney, Marianela

    2013-03-01

    Rhizobium radiobacter is a Gram-negative, nitrogen-fixing bacterium, which is found mainly on the ground. It rarely causes infections in humans. It has been associated with bacteremia, secondary to colonization of intravascular catheters, in immunocompromised patients. The aim of this paper was to report the case of an infective endocarditis caused by R. radiobacter, in a 47-year-old male, diagnosed with chronic kidney disease stage 5, on replacement therapy with hemodialysis and who attended the medical center with fever of two weeks duration. The patient was hospitalized and samples of peripheral blood were taken for culture. Empirical antibiotic therapy was started with cefotaxime plus vancomycin. The transthoracic echocardiogram revealed fusiform vegetation on the tricuspid valve, with grade III-IV/IV regurgitation. On the seventh day after the start of antibiotic therapy, the patient had a clinical and paraclinical improvement. The bacterium identified by blood culture was Rhizobium radiobacter, ceftriaxone-resistant and sensitive to imipenem, amikacin, ampicillin and ampicillin/sulbactam. Because of the clinical improvement, it was decided to continue treatment with vancomycin and additionally, with imipenem. At 14 days after the start of antibiotic therapy, the patient was discharged with outpatient treatment with imipenem up to six weeks of treatment. The control echocardiogram showed the absence of vegetation on the tricuspid valve. This case suggests that R. radiobacter can cause endocarditis in patients with intravascular catheters. PMID:23781714

  13. A partial phylogenetic analysis of the "flavobacter-bacteroides" phylum: basis for taxonomic restructuring

    NASA Technical Reports Server (NTRS)

    Gherna, R.; Woese, C. R.

    1992-01-01

    On the basis of small subunit rRNA sequence analyses five major subgroups within the flavobacteria-bacteroides phylum have been defined. These are tentatively designated the cytophaga subgroup (comprising largely Cytophaga species), the flavobacter subgroup (comprising the true flavobacteria and the polyphyletic genus Weeksella), the bacteroides subgroup (comprising the bacteroides and certain cytophaga-like bacteria), the sphingobacter subgroup (which contains the known sphingolipid-producing members of the phylum), and the saprospira subgroup (comprising particular species of Flexibacter, Flavobacterium, Haliscomenobacter, and, of course, the genus Saprospira). These groupings are given not only by evolutionary distance analysis, but can be defined and distinguished on the basis of a simple small subunit rRNA signatures.

  14. Migration and chemiluminescence of polymorphonuclear cells and monocytes to Bacteroides sonicates.

    PubMed

    Fotos, P G; Lewis, D M; Gerencser, V F; Gerencser, M A; Snyder, I S

    1992-01-01

    Recent investigations have demonstrated that various preparations obtained from representatives of the genus Bacteroides are poorly phagocytized by polymorphonuclear cells (PMN) and macrophages. Crude cell sonicates derived from Bacteroides have been examined for their ability to inhibit migration of PMN and monocytes using a modified migration under agarose in vitro assay. B. gingivalis and B. intermedius were found to be inhibitors of such migration while B. asaccharolyticus did not share this property (P less than 0.005). In addition, B. intermedius sonicates were found to inhibit PMN chemiluminescence to known stimulants (P less than 0.001). These data were not found to result from direct sonicate cytotoxicity and therefore lend additional support to the etiologic importance of specific Bacteroides strains in the pathogenesis of acute and chronic dentoalveolar infections. PMID:1321583

  15. A novel strain of Bacteroides fragilis enhances phagocytosis and polarises M1 macrophages

    PubMed Central

    Deng, Huimin; Li, Zhengchao; Tan, Yafang; Guo, Zhaobiao; Liu, Yangyang; Wang, Ye; Yuan, Yuan; Yang, Ruifu; Bi, Yujing; Bai, Yang; Zhi, Fachao

    2016-01-01

    Commensal Bacteroides fragilis possesses immune-regulatory characteristics. Consequently, it has been proposed as a potential novel probiotic because of its therapeutic effects on immune imbalance, mental disorders and inflammatory diseases. Macrophages play a central role in the immune response, developing either a classical-M1 or an alternative-M2 phenotype after stimulation with various signals. The interactions between macrophages and B. fragilis, however, remain to be defined. Here, a new isolate of B. fragilis, ZY-312, was shown to possess admirable properties, including tolerance to simulated gastric fluid, intestinal fluid and ox bile, and good safety (MOI = 100, 200) and adherent ability (MOI = 100) to LoVo cells. Isolate ZY-312 cell lysate promoted phagocytosis of fluorescent microspheres and pathogenic bacteria in bone marrow-derived macrophage (BMDM) cells. Gene expression of IL-12, iNOS and IL-1β in BMDM cells was increased after treatment with ZY-312, indicating the induction of M1 macrophages, consistent with enhanced secretion of NO. Cell surface expression of CD80 and CD86 was also increased. This study is the first to demonstrate that B. fragilis enhances the phagocytic functions of macrophages, polarising them to an M1 phenotype. Our findings provide insight into the close relationship between B. fragilis and the innate immune system. PMID:27381366

  16. A novel strain of Bacteroides fragilis enhances phagocytosis and polarises M1 macrophages.

    PubMed

    Deng, Huimin; Li, Zhengchao; Tan, Yafang; Guo, Zhaobiao; Liu, Yangyang; Wang, Ye; Yuan, Yuan; Yang, Ruifu; Bi, Yujing; Bai, Yang; Zhi, Fachao

    2016-01-01

    Commensal Bacteroides fragilis possesses immune-regulatory characteristics. Consequently, it has been proposed as a potential novel probiotic because of its therapeutic effects on immune imbalance, mental disorders and inflammatory diseases. Macrophages play a central role in the immune response, developing either a classical-M1 or an alternative-M2 phenotype after stimulation with various signals. The interactions between macrophages and B. fragilis, however, remain to be defined. Here, a new isolate of B. fragilis, ZY-312, was shown to possess admirable properties, including tolerance to simulated gastric fluid, intestinal fluid and ox bile, and good safety (MOI = 100, 200) and adherent ability (MOI = 100) to LoVo cells. Isolate ZY-312 cell lysate promoted phagocytosis of fluorescent microspheres and pathogenic bacteria in bone marrow-derived macrophage (BMDM) cells. Gene expression of IL-12, iNOS and IL-1β in BMDM cells was increased after treatment with ZY-312, indicating the induction of M1 macrophages, consistent with enhanced secretion of NO. Cell surface expression of CD80 and CD86 was also increased. This study is the first to demonstrate that B. fragilis enhances the phagocytic functions of macrophages, polarising them to an M1 phenotype. Our findings provide insight into the close relationship between B. fragilis and the innate immune system. PMID:27381366

  17. Monoculture parameters successfully predict coculture growth kinetics of Bacteroides thetaiotaomicron and two Bifidobacterium strains.

    PubMed

    Van Wey, A S; Cookson, A L; Roy, N C; McNabb, W C; Soboleva, T K; Shorten, P R

    2014-11-17

    Microorganisms rarely live in isolation but are most often found in a consortium. This provides the potential for cross-feeding and nutrient competition among the microbial species, which make it challenging to predict the growth kinetics in coculture. In this paper we developed a mathematical model to describe substrate consumption and subsequent microbial growth and metabolite production for bacteria grown in monoculture. The model characterized substrate utilization kinetics of 18 Bifidobacterium strains. Some bifidobacterial strains demonstrated preferential degradation of oligofructose in that sugars with low degree of polymerization (DP) (DP≤3 or 4) were metabolized before sugars of higher DP, or vice versa. Thus, we expanded the model to describe the preferential degradation of oligofructose. In addition, we adapted the model to describe the competition between human colonic bacteria Bacteroides thetaiotaomicron LMG 11262 and Bifidobacterium longum LMG 11047 or Bifidobacterium breve Yakult for inulin as well as cross-feeding of breakdown products from the extracellular hydrolysis of inulin by B. thetaiotaomicron LMG 11262. We found that the coculture growth kinetics could be predicted based on the respective monoculture growth kinetics. Using growth kinetics from monoculture experiments to predict coculture dynamics will reduce the number of in vitro experiments required to parameterize multi-culture models. PMID:25282609

  18. Complete genome sequence of Bacteroides salanitronis type strain (BL78T)

    SciTech Connect

    Gronow, Sabine; Held, Brittany; Lucas, Susan; Lapidus, Alla L.; Glavina Del Rio, Tijana; Nolan, Matt; Tice, Hope; Deshpande, Shweta; Cheng, Jan-Fang; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, N; Mavromatis, K; Pati, Amrita; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne A.; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Brambilla, Evelyne-Marie; Rohde, Manfred; Goker, Markus; Detter, J. Chris; Woyke, Tanja; Bristow, James; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Eisen, Jonathan

    2011-01-01

    Bacteroides salanitronis Lan et al. 2006 is a species of the genus Bacteroides, which belongs to the family Bacteroidaceae. The species is of interest because it was isolated from the gut of a chicken and the growing awareness that the anaerobic microflora of the cecum is of benefit for the host and may impact poultry farming. The 4,308,663 bp long genome consists of a 4.24 Mbp chromosome and three plasmids (6 kbp, 19 kbp, 40 kbp) containing 3,737 protein-coding and 101 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  19. Cloning and characterization of the Bacteroides fragilis metalloprotease toxin gene.

    PubMed Central

    Franco, A A; Mundy, L M; Trucksis, M; Wu, S; Kaper, J B; Sears, C L

    1997-01-01

    Strains of Bacteroides fragilis that produce a ca. 20-kDa heat-labile protein toxin (termed B. fragilis toxin [BFT]) have been associated with diarrheal disease of animals and humans. BFT alters the morphology of intestinal epithelial cells both in vitro and in vivo and stimulates secretion in ligated intestinal segments of rats, rabbits, and lambs. Previous genetic and biochemical data indicated that BFT was a metalloprotease which hydrolyzed G (monomeric) actin, gelatin, and azocoll in vitro. In this paper, the cloning and sequencing of the entire B. fragilis toxin gene (bft) from enterotoxigenic B. fragilis (ETBF) 86-5443-2-2 is reported. The bft gene from this ETBF strain consists of one open reading frame of 1,191 nucleotides encoding a predicted 397-residue holotoxin with a calculated molecular weight of 44,493. Comparison of the predicted BFT protein sequence with the N-terminal amino acid sequence of purified BFT indicates that BFT is most probably synthesized by ETBF strains as a preproprotein. These data predict that BFT is processed to yield a biologically active toxin of 186 residues with a molecular mass of 20.7 kDa which is secreted into the culture supernatant. Analysis of the holotoxin sequence predicts a 20-residue amphipathic region at the carboxy terminus of BFT. Thus, in addition to the metalloprotease activity of BFT, the prediction of an amphipathic domain suggests that oligomerization of BFT may permit membrane insertion of the toxin with creation of a transmembrane pore. Comparison of the sequences available for the bft genes from ETBF 86-5443-2-2 and VPI 13784 revealed two regions of reduced homology. Hybridization of oligonucleotide probes specific for each bft to toxigenic B.fragilis strains revealed that 51 and 49% of toxigenic strains contained the 86-5433-2-2 and VPI 13784 bft genes, respectively. No toxigenic strain hybridized with both probes. We propose that these two subtypes of bft be termed bft-1 (VPI 13784) and bft-2 (86

  20. Survival of Rhizobium phaseoli in coal-based legume inoculants applied to seeds

    SciTech Connect

    Crawford, S.L.; Berryhill, D.L.

    1983-02-01

    Eight coals used as carriers in legume inoculants promoted the survival of Rhizobium phaseoli on pinto bean seeds. Although peat was more protective, most coal-based inoculants provided >10/sup 4/ viable rhizobia per seed after 4 weeks.

  1. (Basis for the competitiveness of Rhizobium japonicum in nodulation of soybean). Progress report, 1984

    SciTech Connect

    Bauer, W.D.; Evans, W.R.

    1984-01-01

    Those characteristics of Rhizobium cells that are most crucial in determining their competitive success when inoculated onto seed in the field are sought. Initial studies of Rhizobium attachment to root surfaces revealed that only a small subpopulation of the cells in an R. japonicum culture are capable of firmly attaching to soybean roots. The size of the attachment-competent subpopulation depends on strain and culture age. Attachment of rhizobia to roots was found to be linearly proportional to the bacterial concentration. The rate of attachment is constant under our conditions for approximately 60 min, then rapidly levels off to approximately zero. Once attached to the root surface, Rhizobium cells seldom spontaneously detach. Rhizobia of several different species all attached comparably well to soybean roots. Attachment of various Rhizobium species to the root hairs of soybean seedlings likewise showed no evidence of host specificity or selectivity. 2 figs., 2 tabs.

  2. Natural variation in symbiotic nitrogen-fixing Rhizobium and Frankia spp.

    PubMed

    Lie, T A; Akkermans, A D; van Egeraat, A W

    1984-01-01

    A description is given of the natural variation in nitrogen-fixing Rhizobium and Frankia spp. strains and the ability to form root nodules on compatible host plants. Arguments are given for the hypothesis that co-evolution has taken place through mutual interaction of host plants and indigenous Rhizobium and Frankia populations in the soil leading to most efficient symbiotic associations. The significance of root nodules as selective enrichment cultures of particular strains in natural and cultivated soils is exemplified by Rhizobium leguminosarum on various ecotypes of Pisum sativum and with Frankia sp. on various actinorhizal plants, in particular Alnus spp., in different geographic regions. The importance of a host-dependent distribution of Rhizobium and Frankia spp. for agriculture and forestry is discussed. PMID:6397130

  3. Expression of Rhizobium leguminosarum CFN42 genes for lipopolysaccharide in strains derived from different R. leguminosarum soil isolates

    SciTech Connect

    Brink, B.A.; Noel, K.D. ); Miller, J.; Carlson, R.W. )

    1990-02-01

    Two mutant derivatives of Rhizobium leguminosarum ANU843 defective in lipopolysaccharide (LPS) were isolated. The LPSs of both mutants lacked O antigen and some sugar residues of the LPS core oligosaccharides. Genetic regions previously cloned from another Rhizobium leguminosarum wild-type isolate, strain CFN42, were used to complement these mutants. One mutant was complemented to give LPS that was apparently identical to the LPS of strain ANU843 in antigenicity, electrophoretic mobility, and sugar composition. The other mutant was complemented by a second CFN42lps genetic region. In this case the resulting LPS contained O-antigen sugars characteristic of donor strain CFN42 and reacted weakly with antiserum against CFN42 cells, but did not react detectably with antiserum against ANU843 cells. Therefore, one of the CFN42 lps genetic regions specifies a function that is conserved between the two R. leguminosarum wild-type isolates, whereas the other region, at least in part, specifies a strain-specific LPS structure. Transfer of these two genetic regions into wild-type strains derived from R. leguminosarum ANU843 and 128C53 gave results consistent with this conclusion. The mutants derived from strain ANU843 elicited incompletely developed clover nodules that exhibited low bacterial populations and very low nitrogenase activity. Both mutants elicited normally developed, nitrogen-fixing clover nodules when they carried CFN42 lps DNA that permitted synthesis of O-antigen-containing LPS, regardless of whether the O antigen was the one originally made by strain ANU843.

  4. The celC gene, a new phylogenetic marker useful for taxonomic studies in Rhizobium.

    PubMed

    Robledo, Marta; Velázquez, Encarna; Ramírez-Bahena, Martha Helena; García-Fraile, Paula; Pérez-Alonso, Ana; Rivas, Raúl; Martínez-Molina, Eustoquio; Mateos, Pedro F

    2011-09-01

    The celC gene codifies for a cellulase that fulfils a very significant role in the infection process of clover by Rhizobium leguminosarum. This gene is located in the celABC operon present in the chromosome of strains representing R. leguminosarum, Rhizobium etli and Rhizobium radiobacter whose genomes have been completely sequenced. Nevertheless, the existence of this gene in other species of the genus Rhizobium had not been investigated to date. In this study, the celC gene was analysed for the first time in several species of this genus isolated from legume nodules and plant tumours, in order to compare the celC phylogeny to those of other chromosomal and plasmidic genes. The results obtained showed that phylogenies of celC and chromosomal genes, such as rrs, recA and atpD, were completely congruent, whereas no relation was found with symbiotic or virulence genes. Therefore, the suitability and usefulness of the celC gene to differentiate species of the genus Rhizobium, especially those with closely related rrs genes, was highlighted. Consequently, the taxonomic status of several strains of the genus Rhizobium with completely sequenced genomes is also discussed. PMID:21621937

  5. Lipopolysaccharide mutants of Rhizobium meliloti are not defective in symbiosis

    SciTech Connect

    Clover, R.H.; Kieber, J.; Signer, E.R. )

    1989-07-01

    Mutants of Rhizobium meliloti selected primarily for bacteriophage resistance fall into 13 groups. Mutants in the four best-characterized groups (class A, lpsB, lpsC, and class D), which map to the rhizobial chromosome, appear to affect lipopolysaccharide (LPS) as judged by the reactivity with monoclonal antibodies and behavior on sodium dodecyl sulfate-polyacrylamide gels of extracted LPS. Mutations in all 13 groups, in an otherwise wild-type genetic background, are Fix{sup +} on alfalfa. This suggests that LPS does not play a major role in symbiosis. Mutations in lpsB, however, are Fix{sup {minus}} in one particular genetic background, evidently because of the cumulative effect of several independent background mutations. In addition, an auxotrophic mutation evidently equivalent to Escherichia coli carAB is Fix{sup {minus}} on alfalfa.

  6. Acid tolerance of rhizobium trifolii in culture media

    SciTech Connect

    Thornton, F.C.; Davey, C.B.

    1983-01-01

    Tolerance to acidity (pH 4.2 to 4.6), low P (1 to 6 ..mu..M) and high Al (15 to 40..mu..M) for 100 strains of Rhizobium trifolii was assessed in liquid culture media in the laboratory. Response to acidity and Al varied among strains as evidenced by lower maximum cell densities and reduced growth rates, most preceded by a lag phase. Tolerance to acidity did not imply tolerance to Al in all cases. Strains were capable of tolerating higher levels of Al if acidity was reduced. Limitations in rhizobial growth due to low P concentrations were not as severe a stress as high acidity or high Al concentration.

  7. Dechlorination of Atrazine by a Rhizobium sp. Isolate

    PubMed Central

    Bouquard, C.; Ouazzani, J.; Prome, J.; Michel-Briand, Y.; Plesiat, P.

    1997-01-01

    A Rhizobium sp. strain, named PATR, was isolated from an agricultural soil and found to actively degrade the herbicide atrazine. Incubation of PATR in a basal liquid medium containing 30 mg of atrazine liter(sup-1) resulted in the rapid consumption of the herbicide and the accumulation of hydroxyatrazine as the only metabolite detected after 8 days of culture. Experiments performed with ring-labeled [(sup14)C]atrazine indicated no mineralization. The enzyme responsible for the hydroxylation of atrazine was partially purified and found to consist of four 50-kDa subunits. Its synthesis in PATR was constitutive. This new atrazine hydrolase demonstrated 92% sequence identity through a 24-amino-acid fragment with atrazine chlorohydrolase AtzA produced by Pseudomonas sp. strain ADP. PMID:16535552

  8. Nodule initiation elicited by noninfective mutants of Rhizobium phaseoli.

    PubMed

    Vandenbosch, K A; Noel, K D; Kaneko, Y; Newcomb, E H

    1985-06-01

    Rhizobium phaseoli CE106, CE110, and CE115, originally derived by transposon mutagenesis (Noel et al., J. Bacteriol. 158:149-155, 1984), induced the formation of uninfected root nodule-like swellings on bean (Phaseolus vulgaris). Bacteria densely colonized the root surface, and root hair curling and initiation of root cortical-cell divisions occurred normally in mutant-inoculated seedlings, although no infection threads formed. The nodules were ineffective, lacked leghemoglobin, and were anatomically distinct from normal nodules. Ultrastructural specialization for ureide synthesis, characteristic of legumes that form determinate nodules, was absent. Colony morphology of the mutant strains on agar plates was less mucoid than that of the wild type, and under some cultural conditions, the mutants did not react with Cellufluor, a fluorescent stain for beta-linked polysaccharide. These observations suggest that the genetic lesions in these mutants may be related to extracellular polysaccharide synthesis. PMID:3997785

  9. Rhizobium etli maize populations and their competitiveness for root colonization.

    PubMed

    Rosenblueth, Mónica; Martínez-Romero, Esperanza

    2004-05-01

    Rhizobium etli, which normally forms nitrogen-fixing nodules on Phaseolus vulgaris (common bean), is a natural maize endophyte. The genetic diversity of R. etli strains from bulk soil, bean nodules, the maize rhizosphere, the maize root, and inside stem tissue in traditional fields where maize is intercropped with P. vulgaris-beans was analyzed. Based on plasmid profiles and alloenzymes, it was determined that several R. etli types were preferentially encountered as putative maize endophytes. Some of these strains from maize were more competitive maize-root colonizers than other R. etli strains from the rhizosphere or from bean nodules. The dominant and highly competitive strain Ch24-10 was the most tolerant to 6-methoxy-2-benzoxazolinone (MBOA), a maize antimicrobial compound that is inhibitory to some bacteria and fungi. The R. tropici strain CIAT899, successfully used as inoculant of P. vulgaris, was also found to be a competitive maize endophyte in inoculation experiments. PMID:15024554

  10. DESIGN AND EVALUATION OF BACTEROIDES DNA PROBES FOR THE SPECIFIC DETECTION OF HUMAN FECAL POLLUTION

    EPA Science Inventory

    Because Bacteroides spp. are obligate anaerobes that dominate the human fecal flora, and because some species may live only in the human intestine, these bacteria might be useful to distinguish human from nonhuman sources of fecal pollution. To test this hypothesis, PCR primers s...

  11. A proteomic approach towards understanding the cross talk between Bacteroides fragilis and Bifidobacterium longum in coculture.

    PubMed

    Rios-Covián, David; Sánchez, Borja; Martínez, Noelia; Cuesta, Isabel; Hernández-Barranco, Ana M; de Los Reyes-Gavilán, Clara G; Gueimonde, Miguel

    2016-07-01

    A better understanding of the interactions among intestinal microbes is needed to decipher the complex cross talk that takes place within the human gut. Bacteroides and Bifidobacterium genera are among the most relevant intestinal bacteria, and it has been previously reported that coculturing of these 2 microorganisms affects their survival. Therefore, coculturing of Bifidobacterium longum NB667 and Bacteroides fragilis DSMZ2151 was performed with the aim of unravelling the mechanisms involved in their interaction. To this end, we applied proteomic (2D-DIGE) analyses, and by chromatographic techniques we quantified the bacterial metabolites produced during coincubation. Coculture stimulated the growth of B. longum, retarding that of B. fragilis, with concomitant changes in the production of some proteins and metabolites of both bacteria. The combined culture promoted upregulation of the bifidobacterial pyruvate kinase and downregulation of the Bacteroides phosphoenolpyruvate carboxykinase - 2 enzymes involved in the catabolism of carbohydrates. Moreover, B. fragilis FKBP-type peptidyl-prolyl cis-trans isomerase, a protein with chaperone-like activity, was found to be overproduced in coculture, suggesting the induction of a stress response in this microorganism. This study provides mechanistic data to deepen our understanding of the interaction between Bacteroides and Bifidobacterium intestinal populations. PMID:27156738

  12. Involvement of glutamate in the respiratory metabolism of Bradyrhizobium japonicum bacteroids.

    PubMed

    Salminen, S O; Streeter, J G

    1987-02-01

    Bradyrhizobium japonicum bacteroids were isolated anaerobically and supplied with 14C-labeled succinate, malate, aspartate, or glutamate for periods of up to 60 min in the presence of myoglobin to control the O2 concentration. Succinate and malate were absorbed about twice as rapidly as glutamate and aspartate. Conversion of substrate to CO2 was most rapid for malate, followed by succinate, glutamate, and aspartate. When CO2 production was expressed as a proportion of total carbon taken up, malate was still the most rapidly respired substrate, with 68% of the label absorbed converted to CO2. The comparable values for succinate, glutamate, and aspartate were 37, 50, and 38%, respectively. Considering the fate of labeled substrate not respired, greater than 95% of absorbed glutamate remained as glutamate in the bacteroids. In contrast, from 39 to 66% of the absorbed succinate, malate, or aspartate was converted to glutamate. An increase in the rate of CO2 formation from labeled substrates after 20 min appeared to coincide with a maximum accumulation of label in glutamate. The results indicate the presence of a substantial glutamate pool in bacteroids and the involvement of glutamate in the respiratory metabolism of bacteroids. PMID:2879829

  13. Multidrug-Resistant Bacteroides fragilis Bacteremia in a US Resident: An Emerging Challenge

    PubMed Central

    Parajuli, Sunita; Siegfried, Justin; Dubrovskaya, Yanina; Rahimian, Joseph

    2016-01-01

    We describe a case of Bacteroides fragilis bacteremia associated with paraspinal and psoas abscesses in the United States. Resistance to b-lactam/b-lactamase inhibitors, carbapenems, and metronidazole was encountered despite having a recent travel history to India as the only possible risk factor for multidrug resistance. Microbiological cure was achieved with linezolid, moxifloxacin, and cefoxitin. PMID:27418986

  14. Extensive Mobilome-Driven Genome Diversification in Mouse Gut-Associated Bacteroides vulgatus mpk.

    PubMed

    Lange, Anna; Beier, Sina; Steimle, Alex; Autenrieth, Ingo B; Huson, Daniel H; Frick, Julia-Stefanie

    2016-01-01

    Like many other Bacteroides species, Bacteroides vulgatus strain mpk, a mouse fecal isolate which was shown to promote intestinal homeostasis, utilizes a variety of mobile elements for genome evolution. Based on sequences collected by Pacific Biosciences SMRT sequencing technology, we discuss the challenges of assembling and studying a bacterial genome of high plasticity. Additionally, we conducted comparative genomics comparing this commensal strain with the B. vulgatus type strain ATCC 8482 as well as multiple other Bacteroides and Parabacteroides strains to reveal the most important differences and identify the unique features of B. vulgatus mpk. The genome of B. vulgatus mpk harbors a large and diverse set of mobile element proteins compared with other sequenced Bacteroides strains. We found evidence of a number of different horizontal gene transfer events and a genome landscape that has been extensively altered by different mobilization events. A CRISPR/Cas system could be identified that provides a possible mechanism for preventing the integration of invading external DNA. We propose that the high genome plasticity and the introduced genome instabilities of B. vulgatus mpk arising from the various mobilization events might play an important role not only in its adaptation to the challenging intestinal environment in general, but also in its ability to interact with the gut microbiota. PMID:27071651

  15. Extensive Mobilome-Driven Genome Diversification in Mouse Gut-Associated Bacteroides vulgatus mpk

    PubMed Central

    Lange, Anna; Beier, Sina; Steimle, Alex; Autenrieth, Ingo B.; Huson, Daniel H.; Frick, Julia-Stefanie

    2016-01-01

    Like many other Bacteroides species, Bacteroides vulgatus strain mpk, a mouse fecal isolate which was shown to promote intestinal homeostasis, utilizes a variety of mobile elements for genome evolution. Based on sequences collected by Pacific Biosciences SMRT sequencing technology, we discuss the challenges of assembling and studying a bacterial genome of high plasticity. Additionally, we conducted comparative genomics comparing this commensal strain with the B. vulgatus type strain ATCC 8482 as well as multiple other Bacteroides and Parabacteroides strains to reveal the most important differences and identify the unique features of B. vulgatus mpk. The genome of B. vulgatus mpk harbors a large and diverse set of mobile element proteins compared with other sequenced Bacteroides strains. We found evidence of a number of different horizontal gene transfer events and a genome landscape that has been extensively altered by different mobilization events. A CRISPR/Cas system could be identified that provides a possible mechanism for preventing the integration of invading external DNA. We propose that the high genome plasticity and the introduced genome instabilities of B. vulgatus mpk arising from the various mobilization events might play an important role not only in its adaptation to the challenging intestinal environment in general, but also in its ability to interact with the gut microbiota. PMID:27071651

  16. Effect of salt stress on glycine betaine biosynthesis and catabolism by Medicago sativa bacteroids

    SciTech Connect

    Fougere, F.; Poggi, M.-C.; Le Rudulier, D. )

    1990-05-01

    Previous works have shown that glycine betaine (GB) and choline (Cho) are actively taken up by Medicago sativa bacteroids isolated from 4-week-old nodules. Here, we have investigated the effects of NaCl on the fte of Cho and GB. Bacteroids were incubated in low- or high-salt-medium (0.4 M NaCl) and supplemented with {sup 14}C 1,2-Cho or {sup 14}C 1,2-GB. After 3 hours, radioactivity was measured in CO{sub 2} released, in ethanol-soluble and insoluble fractions. In absence of salt, a low proportion of the labelling was found in soluble fraction: 47 and 19% after Cho or GB supply, respectively. On the contrary, in high-salt-medium, the soluble fraction still contained 85% of the radioactivity with GB corresponding to 92-98%. Both enzymes involved in GB biosynthesis from Cho were studied. Choline oxidase activity was enhanced by 59%, while betainal dehydrogenase activity remained unchanged after bacteroid incubation in high-salt-medium. Thus, GB accumulation in salt-stressed bacteroids would be likely a consequence of a decrease of its catabolism rather than an increase of its biosynthesis.

  17. Bacteroides isolated from four mammalian hosts lack host specific patterns in carbon and nitrogen metabolism

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Within the distal gut of mammals are found trillions of microbes that utilize nutrients from diet, intestinal mucosa, and other gut microbes. 402 isolates of Bacteroides ovatus, B. thetaiotaomicron, and B. xylanisolvens were recovered from cow, goat, human, and pig fecal enrichments with cellulose o...

  18. Near-complete genome sequence of the cellulolytic Bacterium Bacteroides (Pseudobacteroides) cellulosolvens ATCC 35603

    DOE PAGESBeta

    Dassa, Bareket; Utturkar, Sagar M.; Hurt, Richard A.; Klingeman, Dawn Marie; Keller, Martin; Xu, Jian; Reddy, Harish Kumar; Borovok, Ilya; Grinberg, Inna Rozman; Lamed, Raphael; et al

    2015-09-24

    We report the single-contig genome sequence of the anaerobic, mesophilic, cellulolytic bacterium, Bacteroides cellulosolvens. The bacterium produces a particularly elaborate cellulosome system, whereas the types of cohesin-dockerin interactions are opposite of other known cellulosome systems: cell-surface attachment is thus mediated via type-I interactions whereas enzymes are integrated via type-II interactions.

  19. Biosynthesis of Rhizobium meliloti lipooligosaccharide Nod factors: NodA is required for an N-acyltransferase activity

    SciTech Connect

    Atkinson, E.M.; Long, S.R. ); Palcic, M.M.; Hindsgaul, O. )

    1994-08-30

    Rhizobium bacteria synthesize N-acylated [beta]-1,4-N-acetylglucosamine lipooligosaccharides, called Nod factors, which act as morphogenic signal molecules to legume roots during development of nitrogen-fixing nodules. The biosynthesis of Nod factors is genetically dependent upon the nodulation (nod) genes, including the common nod genes nodABC. We used the Rhizobium meliloti NodH sulfotransferase to prepare [sup 35]S-labeled oligosaccharides which served as metabolic tracers for Nod enzyme activities. This approach provides a general method for following chitooligosaccharide modifications. We found nodAB-dependent conversion of N-acetylchitotetraose (chitotetraose) monosulfate into hydrophobic compounds which by chromatographic and chemical tests were equivalent to acylated Nod factors. Sequential incubation of labeled intermediates with Escherichia coli containing either NodA or NodB showed that NodB was required before NodA during Nod factor biosynthesis. The acylation activity was sensitive to oligosaccharide chain length, with chitotetraose serving as a better substrate than chitobiose or chitotriose. We constructed a putative Nod factor intermediate, GlcN-[beta]1,4-(GlcNac)[sub 3], by enzymatic synthesis and labeled it by NodH-mediated sulfation to create a specific metabolic probe. Acylation of this oligosaccharide required only NodA. These results confirm previous reports that NodB is an N-deacetylase and suggest that NodA is an N-acyltransferase. 31 refs., 6 figs.

  20. Alfalfa yield response to inoculation with recombinant strains of Rhizobium meliloti with an extra copy of dctABD and/or modified nifA expression.

    PubMed

    Bosworth, A H; Williams, M K; Albrecht, K A; Kwiatkowski, R; Beynon, J; Hankinson, T R; Ronson, C W; Cannon, F; Wacek, T J; Triplett, E W

    1994-10-01

    The construction of rhizobial strains which increase plant biomass under controlled conditions has been previously reported. However, there is no evidence that these newly constructed strains increase legume yield under agricultural conditions. This work tested the hypothesis that carefully manipulating expression of additional copies of nifA and dctABD in strains of Rhizobium meliloti would increase alfalfa yield in the field. The rationale for this hypothesis is based on the positive regulatory role that nifA plays in the expression of the nif regulon and the fact that a supply of dicarboxylic acids from the plant is required as a carbon and energy source for nitrogen fixation by the Rhizobium bacteroids in the nodule. These recombinant strains, as well as the wild-type strains from which they were derived, are ideal tools to examine the effects of modifying or increasing the expression of these genes on alfalfa biomass. The experimental design comprised seven recombinant strains, two wild-type strains, and an uninoculated control. Each treatment was replicated eight times and was conducted at four field sites in Wisconsin. Recombinant strain RMBPC-2, which has an additional copy of both nifA and dctABD, increased alfalfa biomass by 12.9% compared with the yield with the wild-type strain RMBPC and 17.9% over that in the uninoculated control plot at the site where soil nitrogen and organic matter content was lowest. These increases were statistically significant at the 5% confidence interval for each of the three harvests made during the growing season. Strain RMBPC-2 did increase alfalfa biomass at the Hancock site; however, no other significant increases or decreases in alfalfa biomass were observed with the seven other recombinant strains at that site. At three sites where this experiment was conducted, either native rhizobial populations or soil nitrogen concentrations were high. At these sites, none of the recombinant strains affected yield. We conclude that

  1. Bacteroides paurosaccharolyticus sp. nov., isolated from a methanogenic reactor treating waste from cattle farms.

    PubMed

    Ueki, Atsuko; Abe, Kunihiro; Ohtaki, Yoshimi; Kaku, Nobuo; Watanabe, Kazuya; Ueki, Katsuji

    2011-02-01

    A strictly anaerobic bacterial strain (WK042(T)) was isolated from rice-straw residue in a methanogenic reactor treating waste from cattle farms in Japan. Cells were Gram-staining-negative, non-motile, non-spore-forming rods. Growth was stimulated well by haemin, and was enhanced by cobalamin (vitamin B(12)). Strain WK042(T) utilized arabinose, xylose, glucose, mannose and aesculin as preferred substrates. Maltose, dextrin, glycogen, starch and pectin were also utilized, although growth on these substrates was much slower. The strain produced acetate, propionate and succinate from these saccharides. The strain was slightly alkaliphilic, with optimum growth at pH 7.7. The temperature range for growth was 10-40 °C, the optimum being 35 °C. The strain was sensitive to bile. The major cellular fatty acids were anteiso-C(15 : 0), iso-C(17 : 0) 3-OH and C(15 : 0). Menaquinone 11 (MK-11) was the major respiratory quinone and the genomic DNA G+C content was 41.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed the strain in the phylum Bacteroidetes. Strain WK042(T) was related distantly to the type strains of species in the cluster including Bacteroides massiliensis, Bacteroides vulgatus and Bacteroides dorei (91-92 % 16S rRNA gene sequence similarity). Based on data from the present phylogenetic, physiological and chemotaxonomic analyses, strain WK042(T) is considered to represent a novel species of the genus Bacteroides, for which the name Bacteroides paurosaccharolyticus sp. nov. is proposed. The type strain is WK042(T) (=JCM 15092(T) =DSM 21004(T)). PMID:20348319

  2. The Regulatory Protein RosR Affects Rhizobium leguminosarum bv. trifolii Protein Profiles, Cell Surface Properties, and Symbiosis with Clover.

    PubMed

    Rachwał, Kamila; Boguszewska, Aleksandra; Kopcińska, Joanna; Karaś, Magdalena; Tchórzewski, Marek; Janczarek, Monika

    2016-01-01

    Rhizobium leguminosarum bv. trifolii is capable of establishing a symbiotic relationship with plants from the genus Trifolium. Previously, a regulatory protein encoded by rosR was identified and characterized in this bacterium. RosR possesses a Cys2-His2-type zinc finger motif and belongs to Ros/MucR family of rhizobial transcriptional regulators. Transcriptome profiling of the rosR mutant revealed a role of this protein in several cellular processes, including the synthesis of cell-surface components and polysaccharides, motility, and bacterial metabolism. Here, we show that a mutation in rosR resulted in considerable changes in R. leguminosarum bv. trifolii protein profiles. Extracellular, membrane, and periplasmic protein profiles of R. leguminosarum bv. trifolii wild type and the rosR mutant were examined, and proteins with substantially different abundances between these strains were identified. Compared with the wild type, extracellular fraction of the rosR mutant contained greater amounts of several proteins, including Ca(2+)-binding cadherin-like proteins, a RTX-like protein, autoaggregation protein RapA1, and flagellins FlaA and FlaB. In contrast, several proteins involved in the uptake of various substrates were less abundant in the mutant strain (DppA, BraC, and SfuA). In addition, differences were observed in membrane proteins of the mutant and wild-type strains, which mainly concerned various transport system components. Using atomic force microscopy (AFM) imaging, we characterized the topography and surface properties of the rosR mutant and wild-type cells. We found that the mutation in rosR gene also affected surface properties of R. leguminosarum bv. trifolii. The mutant cells were significantly more hydrophobic than the wild-type cells, and their outer membrane was three times more permeable to the hydrophobic dye N-phenyl-1-naphthylamine. The mutation of rosR also caused defects in bacterial symbiotic interaction with clover plants. Compared with

  3. The Regulatory Protein RosR Affects Rhizobium leguminosarum bv. trifolii Protein Profiles, Cell Surface Properties, and Symbiosis with Clover

    PubMed Central

    Rachwał, Kamila; Boguszewska, Aleksandra; Kopcińska, Joanna; Karaś, Magdalena; Tchórzewski, Marek; Janczarek, Monika

    2016-01-01

    Rhizobium leguminosarum bv. trifolii is capable of establishing a symbiotic relationship with plants from the genus Trifolium. Previously, a regulatory protein encoded by rosR was identified and characterized in this bacterium. RosR possesses a Cys2-His2-type zinc finger motif and belongs to Ros/MucR family of rhizobial transcriptional regulators. Transcriptome profiling of the rosR mutant revealed a role of this protein in several cellular processes, including the synthesis of cell-surface components and polysaccharides, motility, and bacterial metabolism. Here, we show that a mutation in rosR resulted in considerable changes in R. leguminosarum bv. trifolii protein profiles. Extracellular, membrane, and periplasmic protein profiles of R. leguminosarum bv. trifolii wild type and the rosR mutant were examined, and proteins with substantially different abundances between these strains were identified. Compared with the wild type, extracellular fraction of the rosR mutant contained greater amounts of several proteins, including Ca2+-binding cadherin-like proteins, a RTX-like protein, autoaggregation protein RapA1, and flagellins FlaA and FlaB. In contrast, several proteins involved in the uptake of various substrates were less abundant in the mutant strain (DppA, BraC, and SfuA). In addition, differences were observed in membrane proteins of the mutant and wild-type strains, which mainly concerned various transport system components. Using atomic force microscopy (AFM) imaging, we characterized the topography and surface properties of the rosR mutant and wild-type cells. We found that the mutation in rosR gene also affected surface properties of R. leguminosarum bv. trifolii. The mutant cells were significantly more hydrophobic than the wild-type cells, and their outer membrane was three times more permeable to the hydrophobic dye N-phenyl-1-naphthylamine. The mutation of rosR also caused defects in bacterial symbiotic interaction with clover plants. Compared with

  4. Metallo-β-Lactamase-Producing Bacteroides Species Can Shield Other Members of the Gut Microbiota from Antibiotics

    PubMed Central

    Tima, Mary Ann; Nerandzic, Michelle M.

    2014-01-01

    Antibiotics disrupt the intestinal microbiota, rendering patients vulnerable to colonization by exogenous pathogens. Intermicrobial interactions may attenuate this effect. Incubation with ceftriaxone-resistant, ccrA-positive, β-lactamase-producing Bacteroides strains raised the minimum bactericidal concentration of ceftriaxone required to kill a susceptible Escherichia coli strain (mean change, <0.25 to 29 mg/liter; P = 0.009); incubation with ceftriaxone-resistant but non-β-lactamase-producing Bacteroides strains had no effect. The production of β-lactamase by common members of the intestinal microbiota (Bacteroides) can protect susceptible fellow commensals from β-lactams. PMID:25288080

  5. Non-contiguous finished genome sequence and description of Bacteroides neonati sp. nov., a new species of anaerobic bacterium

    PubMed Central

    Cassir, Nadim; Croce, Olivier; Pagnier, Isabelle; Benamar, Samia; Couderc, Carine; Robert, Catherine; Raoult, Didier; La Scola, Bernard

    2014-01-01

    Bacteroides neonati strain MS4T, is the type strain of Bacteroides neonati sp. nov., a new species within the genus Bacteroides. This strain, whose genome is described here, was isolated from a premature neonate stool sample. B. neonati strain MS4T is an obligate anaerobic Gram-negative bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5.03 Mbp long genome exhibits a G+C content of 43.53% and contains 4,415 protein-coding and 91 RNA genes, including 9 rRNA genes. PMID:25197464

  6. Rhizobium taibaishanense sp. nov., isolated from a root nodule of Kummerowia striata.

    PubMed

    Yao, Li Juan; Shen, Yao Yao; Zhan, Jun Peng; Xu, Wei; Cui, Guang Ling; Wei, Ge Hong

    2012-02-01

    During a study of the diversity and phylogeny of rhizobia in the root nodules of Kummerowia striata grown in north-western China, four strains were classified in the genus Rhizobium on the basis of their 16S rRNA gene sequences. The 16S rRNA gene sequences of three of these strains were identical and that of the other strain, which was the only one isolated in Yangling, differed from the others by just 1 bp. The16S rRNA gene sequences of the four strains showed a mean similarity of 99.3 % with the most closely related, recognized species, Rhizobium vitis. The corresponding recA and glnA gene sequences showed similarities with established species of Rhizobium of less than 86.5 % and less than 89.6 %, respectively. These low similarities indicated that the four strains represented a novel species of the genus Rhizobium. The strains were also found to be distinguishable from the closest related, established species (R. vitis) by rep-PCR DNA fingerprinting, analysis of cellular fatty acid profiles and from the results of a series of phenotypic tests. The level of DNA-DNA relatedness between the representative strain CCNWSX 0483(T) and Rhizobium vitis IAM 14140(T) was only 40.13 %. Therefore, a novel species, Rhizobium taibaishanense sp. nov., is proposed, with strain CCNWSX 0483(T) ( = ACCC 14971(T) = HAMBI 3214(T)) as the type strain. In nodulation and pathogenicity tests, none of the four strains of Rhizobium taibaishanense sp. nov. was able to induce any nodule or tumour formation on plants. As no amplicons were detected when DNA from the strains was run in PCR with primers for the detection of nodA, nifH and virC gene sequences, the strains probably do not carry sym or vir genes. PMID:21421926

  7. Characterization of enterotoxigenic Bacteroides fragilis by a toxin-specific enzyme-linked immunosorbent assay.

    PubMed Central

    Van Tassell, R L; Lyerly, D M; Wilkins, T D

    1994-01-01

    Within the past decade, certain strains of Bacteroides fragilis have been associated with diarrhea in humans and cytotoxic activity on certain colon carcinoma cell lines. An enzyme-linked immunosorbent assay (ELISA) for detecting the enterotoxin of B. fragilis in cultures and stools was developed by using high-titer monospecific goat and rabbit antitoxins in an indirect format. The lower limit of detection for purified toxin was approximately 0.05 micrograms/ml; the linear range was from 0.05 to 10 microgram/ml. Using the ELISA to screen cultures of toxigenic and nontoxigenic strains of B. fragilis, we observed 100% correlation with 16 known toxigenic strains which had various cytotoxic activities on HT-29 cells. In addition, we found 6 of 62 previously untested strains also to be positive in both assays. Stability studies revealed that although the cytotoxic activities of crude and purified toxin preparations incubated at elevated temperatures were rapidly lost, the ELISA responses were not significantly reduced. Sodium dodecyl sulfate(SDS)-polyacrylamide gel electrophoresis and SDS-capillary electrophoresis showed that the purified toxin autodigested to several stable peptides. Studies on partially purified membranes from the toxigenic strains revealed the presence of several membrane-associated components which were noncytotoxic but strongly immunoreactive in the ELISA. Preliminary studies with spiked feces indicated that the ELISA may be useful for screening not only cultures for the enterotoxigenic B. fragilis but also stool specimens. Ongoing studies are focusing on determining the nature of the toxin's apparent proteolytic capabilities and investigating the feasibility of using the ELISA on stool specimens from healthy and diarrheic humans. Images PMID:8556504

  8. Nitrogen-fixing Rhizobium-legume symbiosis: are polyploidy and host peptide-governed symbiont differentiation general principles of endosymbiosis?

    PubMed Central

    Maróti, Gergely; Kondorosi, Éva

    2014-01-01

    The symbiosis between rhizobia soil bacteria and legumes is facultative and initiated by nitrogen starvation of the host plant. Exchange of signal molecules between the partners leads to the formation of root nodules where bacteria are converted to nitrogen-fixing bacteroids. In this mutualistic symbiosis, the bacteria provide nitrogen sources for plant growth in return for photosynthates from the host. Depending on the host plant the symbiotic fate of bacteria can either be reversible or irreversible. In Medicago plants the bacteria undergo a host-directed multistep differentiation process culminating in the formation of elongated and branched polyploid bacteria with definitive loss of cell division ability. The plant factors are nodule-specific symbiotic peptides. About 500 of them are cysteine-rich NCR peptides produced in the infected plant cells. NCRs are targeted to the endosymbionts and the concerted action of different sets of peptides governs different stages of endosymbiont maturation. This review focuses on symbiotic plant cell development and terminal bacteroid differentiation and demonstrates the crucial roles of symbiotic peptides by showing an example of multi-target mechanism exerted by one of these symbiotic peptides. PMID:25071739

  9. Rhizobium cellulase CelC2 is essential for primary symbiotic infection of legume host roots

    PubMed Central

    Robledo, M.; Jiménez-Zurdo, J. I.; Velázquez, E.; Trujillo, M. E.; Zurdo-Piñeiro, J. L.; Ramírez-Bahena, M. H.; Ramos, B.; Díaz-Mínguez, J. M.; Dazzo, F.; Martínez-Molina, E.; Mateos, P. F.

    2008-01-01

    The rhizobia–legume, root-nodule symbiosis provides the most efficient source of biologically fixed ammonia fertilizer for agricultural crops. Its development involves pathways of specificity, infectivity, and effectivity resulting from expressed traits of the bacterium and host plant. A key event of the infection process required for development of this root-nodule symbiosis is a highly localized, complete erosion of the plant cell wall through which the bacterial symbiont penetrates to establish a nitrogen-fixing, intracellular endosymbiotic state within the host. This process of wall degradation must be delicately balanced to avoid lysis and destruction of the host cell. Here, we describe the purification, biochemical characterization, molecular genetic analysis, biological activity, and symbiotic function of a cell-bound bacterial cellulase (CelC2) enzyme from Rhizobium leguminosarum bv. trifolii, the clover-nodulating endosymbiont. The purified enzyme can erode the noncrystalline tip of the white clover host root hair wall, making a localized hole of sufficient size to allow wild-type microsymbiont penetration. This CelC2 enzyme is not active on root hairs of the nonhost legume alfalfa. Microscopy analysis of the symbiotic phenotypes of the ANU843 wild type and CelC2 knockout mutant derivative revealed that this enzyme fulfils an essential role in the primary infection process required for development of the canonical nitrogen-fixing R. leguminosarum bv. trifolii-white clover symbiosis. PMID:18458328

  10. Nodules Initiated by Rhizobium meliloti Exopolysaccharide Mutants Lack a Discrete, Persistent Nodule Meristem 1

    PubMed Central

    Yang, Cheng; Signer, Ethan R.; Hirsch, Ann M.

    1992-01-01

    Infection of alfalfa with Rhizobium meliloti exo mutants deficient in exopolysaccharide results in abnormal root nodules that are devoid of bacteria and fail to fix nitrogen. Here we report further characterization of these abnormal nodules. Tightly curled root hairs or shepherd's crooks were found after inoculation with Rm 1021-derived exo mutants, but curling was delayed compared with wild-type Rm 1021. Infection threads were initiated in curled root hairs by mutants as well as by wild-type R. meliloti, but the exo mutant-induced threads aborted within the peripheral cells of the developing nodule. Also, nodules elicited by Rm 1021-derived exo mutants were more likely to develop on secondary roots than on the primary root. In contrast with wild-type R. meliloti-induced nodules, the exo mutant-induced nodules lacked a well defined apical meristem, presumably due to the abortion of the infection threads. The relationship of these findings to the physiology of nodule development is discussed. ImagesFigure 3Figure 1Figure 2Figure 4 PMID:16668605

  11. Enhanced nitrogen fixation in a Rhizobium etli ntrC mutant that overproduces the Bradyrhizobium japonicum symbiotic terminal oxidase cbb{sub 3}

    SciTech Connect

    Soberon, M.; Lopez, O.; Morera, C.; Girard, M.L.; Tabche, M.L.; Miranda, J.

    1999-05-01

    The ntrC gene codes for a transcriptional activator protein that modulates gene expression in response to nitrogen. The cytochrome production pattern of a Rhizobium etli ntrC mutant (CFN2012) was studied. CO difference spectral analysis of membranes showed that CFN2012 produced a terminal oxidase similar to the symbiotic terminal oxidase of bacteroids in free-living cells under aerobic conditions, with a characteristic trough at 553 nm. CFN2012 produced two c-type cytochromes with molecular masses of 27 and 32 kDa in contrast with the wild-type strain, which produced only a 32-kDa c-tye cytochrome. The expression levels of the R. etli fix/NOQP operon, which codes for terminal oxidase cbb{sub 3}, were not affected by the ntrC mutation. However, the production levels of the two c-type cytochromes (27 and 32 kDa) were enhanced at least eightfold when the Bradyrhizobium japonicum fixNOQP operon was expressed in CFN2012 from the nptII promoter (pMSfix{sup c}), suggesting that these proteins are subunits FixO (27 kDa) and FixP (32 kDa) of cbb{sub 3} and that CFN2012/pMSfix{sup c} overproduced this terminal oxidase. CFN2012/pMSfix{sup c} showed a significant increase in its symbiotic performance as judged by the determination of nitrogenase activities of plants inoculated with this strain, suggesting that the overproduction of cbb{sub 3} terminal oxidase correlates with an enhancement in symbiotic nitrogen fixation.

  12. Maturation of Rhizobium leguminosarum Hydrogenase in the Presence of Oxygen Requires the Interaction of the Chaperone HypC and the Scaffolding Protein HupK*

    PubMed Central

    Albareda, Marta; Pacios, Luis F.; Manyani, Hamid; Rey, Luis; Brito, Belén; Imperial, Juan; Ruiz-Argüeso, Tomás; Palacios, Jose M.

    2014-01-01

    [NiFe] hydrogenases are key enzymes for the energy and redox metabolisms of different microorganisms. Synthesis of these metalloenzymes involves a complex series of biochemical reactions catalyzed by a plethora of accessory proteins, many of them required to synthesize and insert the unique NiFe(CN)2CO cofactor. HypC is an accessory protein conserved in all [NiFe] hydrogenase systems and involved in the synthesis and transfer of the Fe(CN)2CO cofactor precursor. Hydrogenase accessory proteins from bacteria-synthesizing hydrogenase in the presence of oxygen include HupK, a scaffolding protein with a moderate sequence similarity to the hydrogenase large subunit and proposed to participate as an intermediate chaperone in the synthesis of the NiFe cofactor. The endosymbiotic bacterium Rhizobium leguminosarum contains a single hydrogenase system that can be expressed under two different physiological conditions: free-living microaerobic cells (∼12 μm O2) and bacteroids from legume nodules (∼10–100 nm O2). We have used bioinformatic tools to model HupK structure and interaction of this protein with HypC. Site-directed mutagenesis at positions predicted as critical by the structural analysis have allowed the identification of HupK and HypC residues relevant for the maturation of hydrogenase. Mutant proteins altered in some of these residues show a different phenotype depending on the physiological condition tested. Modeling of HypC also predicts the existence of a stable HypC dimer whose presence was also demonstrated by immunoblot analysis. This study widens our understanding on the mechanisms for metalloenzyme biosynthesis in the presence of oxygen. PMID:24942742

  13. Rhizobium grahamii sp. nov., from nodules of Dalea leporina, Leucaena leucocephala and Clitoria ternatea, and Rhizobium mesoamericanum sp. nov., from nodules of Phaseolus vulgaris, siratro, cowpea and Mimosa pudica.

    PubMed

    López-López, Aline; Rogel-Hernández, Marco A; Barois, Isabelle; Ortiz Ceballos, Angel I; Martínez, Julio; Ormeño-Orrillo, Ernesto; Martínez-Romero, Esperanza

    2012-09-01

    Two novel related Rhizobium species, Rhizobium grahamii sp. nov. and Rhizobium mesoamericanum sp. nov., were identified by a polyphasic approach using DNA-DNA hybridization, whole-genome sequencing and phylogenetic and phenotypic characterization including nodulation of Leucaena leucocephala and Phaseolus vulgaris (bean). As similar bacteria were found in the Los Tuxtlas rainforest in Mexico and in Central America, we suggest the existence of a Mesoamerican microbiological corridor. The type strain of Rhizobium grahamii sp. nov. is CCGE 502(T) (= ATCC BAA-2124(T) = CFN 242(T) = Dal4(T) = HAMBI 3152(T)) and that of Rhizobium mesoamericanum sp. nov. is CCGE 501(T) (= ATCC BAA-2123(T) = HAMBI 3151(T) = CIP 110148(T) = 1847(T)). PMID:22081714

  14. Rhizobium sp. strain BN4 (a selenium oxyanion-reducing bacterium) 16S rRNA gene complete sequence

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study used 1482 base pair 16S rRNA gene sequence methods in conjunction with other biochemical and morphological studies to confirm the identification of a bacterium (refer to as the BN4 strain) as a Rhizobium sp. The 16S rRNA gene sequence places it with the Rhizobium clade that includes R. d...

  15. Characterization of the N2O-producing soil bacterium Rhizobium azooxidifex sp. nov.

    PubMed

    Behrendt, Undine; Kämpfer, Peter; Glaeser, Stefanie P; Augustin, Jürgen; Ulrich, Andreas

    2016-06-01

    In the context of studying the bacterial community involved in nitrogen transformation processes in arable soils exposed to different extents of erosion and sedimentation in a long-term experiment (CarboZALF), a strain was isolated that reduced nitrate to nitrous oxide without formation of molecular nitrogen. The presence of the functional gene nirK, encoding the respiratory copper-containing nitrite reductase, and the absence of the nitrous oxide reductase gene nosZ indicated a truncated denitrification pathway and that this bacterium may contribute significantly to the formation of the important greenhouse gas N2O. Phylogenetic analysis based on the 16S rRNA gene sequence and the housekeeping genes recA and atpD demonstrated that the investigated soil isolate belongs to the genus Rhizobium. The closest phylogenetic neighbours were the type strains of Rhizobium. subbaraonis and Rhizobium. halophytocola. The close relationship with R. subbaraonis was reflected by similarity analysis of the recA and atpD genes and their amino acid positions. DNA-DNA hybridization studies revealed genetic differences at the species level, which were substantiated by analysis of the whole-cell fatty acid profile and several distinct physiological characteristics. Based on these results, it was concluded that the soil isolate represents a novel species of the genus Rhizobium, for which the name Rhizobium azooxidifex sp. nov. (type strain Po 20/26T=DSM 100211T=LMG 28788T) is proposed. PMID:27030972

  16. The structure of legume-rhizobium interaction networks and their response to tree invasions.

    PubMed

    Le Roux, Johannes J; Mavengere, Natasha R; Ellis, Allan G

    2016-01-01

    Establishing mutualistic interactions in novel environments is important for the successful establishment of some non-native plant species. These associations may, in turn, impact native species interaction networks as non-natives become dominant in their new environments. Using phylogenetic and ecological interaction network approaches we provide the first report of the structure of belowground legume-rhizobium interaction networks and how they change along a gradient of invasion (uninvaded, semi invaded and heavily invaded sites) by Australian Acacia species in South Africa's Cape Floristic Region. We found that native and invasive legumes interact with distinct rhizobial lineages, most likely due to phylogenetic uniqueness of native and invasive host plants. Moreover, legume-rhizobium interaction networks are not nested, but significantly modular with high levels of specialization possibly as a result of legume-rhizobium co-evolution. Although network topology remained constant across the invasion gradient, composition of bacterial communities associated with native legumes changed dramatically as acacias increasingly dominated the landscape. In stark contrast to aboveground interaction networks (e.g. pollination and seed dispersal) we show that invasive legumes do not infiltrate existing native legume-rhizobium networks but rather form novel modules. This absence of mutualist overlap between native and invasive legumes suggests the importance of co-invading rhizobium-acacia species complexes for Acacia invasion success, and argues against a ubiquitous role for the formation and evolutionary refinement of novel interactions. PMID:27255514

  17. Two host-inducible genes of Rhizobium fredii and characterization of the inducing compound.

    PubMed Central

    Sadowsky, M J; Olson, E R; Foster, V E; Kosslak, R M; Verma, D P

    1988-01-01

    Random transcription fusions with Mu d1(Kan lac) generated three mutants in Rhizobium fredii (strain USDA 201) which showed induction of beta-galactosidase when grown in root exudate of the host plants Glycine max, Phaseolus vulgaris, and Vigna ungliculata. Two genes were isolated from a library of total plasmid DNA of one of the mutants, 3F1. These genes, present in tandem on a 4.2-kilobase HindIII fragment, appear in one copy each on the symbiotic plasmid and do not hybridize to the Rhizobium meliloti common nodulation region. They comprise two separate transcriptional units coding for about 450 and 950 nucleotides, both of which are transcribed in the same direction. The two open reading frames are separated by 586 base pairs, and the 5H regions of the two genes show a common sequence. No similarity was found with the promoter areas of Rhizobium trifolii, R. meliloti, or Bradyrhizobium japonicum nif genes and with any known nodulation genes. Regions homologous to both sequences were detected in EcoRI digests of genomic DNAs from B. japonicum USDA 110, USDA 122, and 61A76, but not in genomic DNA from R. trifolii, Rhizobium leguminosarum, or Rhizobium phaseoli. Mass spectrometry and nuclear magnetic resonance analysis indicated that the inducing compound has properties of 4',7-dihydroxyisoflavone, daidzein. These results suggest that, in addition to common nodulation genes, several other genes appear to be specifically induced by compounds in the root exudate of the host plants. Images PMID:2447061

  18. Rhizobium oryzicola sp. nov., potential plant-growth-promoting endophytic bacteria isolated from rice roots.

    PubMed

    Zhang, Xiao-Xia; Gao, Ju-Sheng; Cao, Yan-Hua; Sheirdil, Rizwan Ali; Wang, Xiu-Cheng; Zhang, Lei

    2015-09-01

    Bacterial strains ZYY136(T) and ZYY9 were isolated from surface-sterilized rice roots from a long-term experiment of rice-rice--Astragalus sinicus rotation. The 16S rRNA gene sequences of strains ZYY136(T) and ZYY9 showed the highest similarity, of 97.0%, to Rhizobium tarimense PL-41(T). Sequence analysis of the housekeeping genes recA, thrC and atpD clearly differentiated the isolates from currently described species of the genus Rhizobium. The DNA-DNA relatedness value between ZYY136(T) and ZYY9 was 82.3%, and ZYY136(T) showed 34.0% DNA-DNA relatedness with the most closely related type strain, R. tarimense PL-41(T). The DNA G+C content of strain ZYY136(T) was 58.1 mol%. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0 and C16 : 0 3-OH. Strains ZYY136(T) and ZYY9 could be differentiated from the previously defined species of the genus Rhizobium by several phenotypic characteristics. Therefore, we conclude that strains ZYY136(T) and ZYY9 represent a novel species of the genus Rhizobium, for which the name Rhizobium oryzicola sp. nov. is proposed (type strain ZYY136(T) = ACCC 05753(T) = KCTC 32088(T)). PMID:26016492

  19. Mapping the Genetic Basis of Symbiotic Variation in Legume-Rhizobium Interactions in Medicago truncatula

    PubMed Central

    Gorton, Amanda J.; Heath, Katy D.; Pilet-Nayel, Marie-Laure; Baranger, Alain

    2012-01-01

    Mutualisms are known to be genetically variable, where the genotypes differ in the fitness benefits they gain from the interaction. To date, little is known about the loci that underlie such genetic variation in fitness or whether the loci influencing fitness are partner specific, and depend on the genotype of the interaction partner. In the legume-rhizobium mutualism, one set of potential candidate genes that may influence the fitness benefits of the symbiosis are the plant genes involved in the initiation of the signaling pathway between the two partners. Here we performed quantitative trait loci (QTL) mapping in Medicago truncatula in two different rhizobium strain treatments to locate regions of the genome influencing plant traits, assess whether such regions are dependent on the genotype of the rhizobial mutualist (QTL × rhizobium strain), and evaluate the contribution of sequence variation at known symbiosis signaling genes. Two of the symbiotic signaling genes, NFP and DMI3, colocalized with two QTL affecting average fruit weight and leaf number, suggesting that natural variation in nodulation genes may potentially influence plant fitness. In both rhizobium strain treatments, there were QTL that influenced multiple traits, indicative of either tight linkage between loci or pleiotropy, including one QTL with opposing effects on growth and reproduction. There was no evidence for QTL × rhizobium strain or genotype × genotype interactions, suggesting either that such interactions are due to small-effect loci or that more genotype-genotype combinations need to be tested in future mapping studies. PMID:23173081

  20. Marsh soils as potential sinks for Bacteroides fecal indicator bacteria, Waccamaw National Wildlife Refuge, Georgetown, SC, USA

    USGS Publications Warehouse

    Drexler, Judith Z.; Johnson, Heather E.; Duris, Joseph W.; Krauss, Ken W.

    2014-01-01

    A soil core collected in a tidal freshwater marsh in the Waccamaw National Wildlife Refuge (Georgetown, SC) exuded a particularly strong odor of cow manure upon extrusion. In order to test for manure and determine its provenance, we carried out microbial source tracking using DNA markers for Bacteroides, a noncoliform, anaerobic bacterial group that represents a broad group of the fecal population. Three core sections from 0-3 cm, 9-12 cm and 30-33 were analyzed for the presence of Bacteroides. The ages of core sediments were estimated using 210Pb and 137Cs dating. All three core sections tested positive for Bacteroides DNA markers related to cow or deer feces. Because cow manure is stockpiled, used as fertilizer, and a source of direct contamination in the Great Pee Dee River/Winyah Bay watershed, it is very likely the source of the Bacteroides that was deposited on the marsh. The mid-points of the core sections were dated as follows: 0-3 cm: 2009; 9-12 cm: 1999, and 30-33 cm: 1961. The presence of Bacteroides at different depths/ages in the soil profile indicates that soils in tidal freshwater marshes are, at the least, capable of being short-term sinks for Bacteroides and, may have the potential to be long-term sinks of stable, naturalized populations.

  1. Inhibition of ribonucleic acid polymerase by a bacteriocin from Bacteroides fragilis.

    PubMed Central

    Mossie, K G; Robb, F T; Jones, D T; Woods, D R

    1981-01-01

    The Bacteroides fragilis bacteriocin which inhibits ribonucleic acid (RNA) polymerase activity had a narrow activity spectrum in vivo and only inhibited the growth of certain B. fragilis strains. In vitro the bacteriocin was not specific and inhibited RNA polymerases from widely diverse bacterial genera. RNA polymerases from rifampin-resistant strains of Bacteroides thetaiotaomicron and Clostridium acetobutylicum were resistant to the bacteriocin in vitro. Purified bacteriocin bound to partially purified RNA polymerase, and both proteins were cosedimented in a glycerol gradient. In the RNA polymerase reaction, the bacteriocin acted as a competitive inhibitor for adenosine, cytidine, and uridine 5'-triphosphates and as a noncompetitive inhibitor for guanosine 5'-triphosphate. The bacteriocin did not inhibit RNA polymerase from chicken embryos. PMID:6177280

  2. Metronidazole- and Carbapenem-Resistant Bacteroides thetaiotaomicron Isolated in Rochester, Minnesota, in 2014

    PubMed Central

    Sadarangani, Sapna P.; Cunningham, Scott A.; Jeraldo, Patricio R.; Wilson, John W.; Khare, Reeti

    2015-01-01

    Emerging antimicrobial resistance in members of the Bacteroides fragilis group is a concern in clinical medicine. Although metronidazole and carbapenem resistance have been reported in Bacteroides thetaiotaomicron, a member of the B. fragilis group, they have not, to the best of our knowledge, been reported together in the same B. thetaiotaomicron isolate. Herein, we report isolation of piperacillin-tazobactam-, metronidazole-, clindamycin-, ertapenem-, and meropenem-resistant B. thetaiotaomicron from a patient with postoperative intra-abdominal abscess and empyema. Whole-genome sequencing demonstrated the presence of nimD with at least a portion of IS1169 upstream, a second putative nim gene, two β-lactamase genes (one of which has not been previously reported), two tetX genes, tetQ, ermF, two cat genes, and a number of efflux pumps. This report highlights emerging antimicrobial resistance in B. thetaiotaomicron and the importance of identification and antimicrobial susceptibility testing of selected anaerobic bacteria. PMID:25941219

  3. Bacteroides in the Infant Gut Consume Milk Oligosaccharides via Mucus-Utilization Pathways

    PubMed Central

    Marcobal, A.; Barboza, M.; Sonnenburg, E.D.; Pudlo, N.; Martens, E.C.; Desai, P.; Lebrilla, C.B.; Weimer, B.C.; Mills, D.A.; German, J.B.; Sonnenburg, J.L.

    2011-01-01

    Summary Newborns are colonized with an intestinal microbiota shortly after birth but the factors governing the retention and abundance of specific microbial lineages are unknown. Nursing infants consume human milk oligosaccharides (HMOs) that pass undigested to the distal gut where they may be digested by microbes. We determined that the prominent neonate gut residents, Bacteroides thetaiotaomicron and Bacteroides fragilis, induce the same genes during HMO consumption that are used to harvest host mucus glycans, which are structurally similar to HMOs. Lacto-N-neotetraose, a specific HMO component, selects for HMO-adapted species such as Bifidobacterium infantis, which cannot use mucus, and provides a selective advantage to B. infantis in vivo when bi-associated with B. thetaiotaomicron in the gnotobiotic mouse gut. This indicates that the complex oligosaccharide mixture within HMOs attracts both mutualistic mucus-adapted species and HMO-adapted bifidobacteria to the infant intestine that likely facilitate both milk and future solid food digestion. PMID:22036470

  4. Complete genome sequence of Bacteroides helcogenes type strain (P 36-108T)

    SciTech Connect

    Pati, Amrita; Gronow, Sabine; Zeytun, Ahmet; Lapidus, Alla L.; Nolan, Matt; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, N; Mavromatis, K; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Detter, J. Chris; Brambilla, Evelyne-Marie; Rohde, Manfred; Goker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Lucas, Susan

    2011-01-01

    Bacteroides helcogenes Benno et al. 1983 is of interest because of its isolated phylogenetic location and, although it has been found in pig feces and is known to be pathogenic for pigs, occurrence of this bacterium is rare and it does not cause significant damage in intensive animal husbandry. The genome of B. helcogenes P 36-108T is already the fifth completed and published type strain genome from the genus Bacteroides in the family Bacteroidaceae. The 3,998,906 bp long genome with its 3,353 protein-coding and 83 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  5. Characterization of bactericidal activity of clindamycin against Bacteroides fragilis via kill curve methods.

    PubMed Central

    Klepser, M E; Banevicius, M A; Quintiliani, R; Nightingale, C H

    1996-01-01

    Kill curves were determined for five isolates of Bacteroides fragilis with clindamycin at concentrations equal to the MIC or to 4, 16, and 64 times the MIC. Examination of plots of log CFU per milliliter versus time revealed no association between the clindamycin concentration and the rate and extent of the bactericidal activity against B. fragilis at or below 64 times the MIC. PMID:8843310

  6. Polysaccharide synthesis in relation to nodulation behavior of Rhizobium leguminosarum.

    PubMed Central

    Breedveld, M W; Cremers, H C; Batley, M; Posthumus, M A; Zevenhuizen, L P; Wijffelman, C A; Zehnder, A J

    1993-01-01

    In this study, we characterized four Tn5 mutants derived from Rhizobium leguminosarum RBL5515 with respect to synthesis and secretion of cellulose fibrils, extracellular polysaccharides (EPS), capsular polysaccharides, and cyclic beta-(1,2)-glucans. One mutant, strain RBL5515 exo-344::Tn5, synthesizes residual amounts of EPS, the repeating unit of which lacks the terminal galactose molecule and the substituents attached to it. On basis of the polysaccharide production pattern of strain RBL5515 exo-344::Tn5, the structural features of the polysaccharides synthesized, and the results of an analysis of the enzyme activities involved, we hypothesize that this strain is affected in a galactose transferase involved in the synthesis of EPS only. All four mutants failed to nodulate plants belonging to the pea cross-inoculation group; on Vicia sativa they induced root hair deformation and rare abortive infection threads. All of the mutants appeared to be pleiotropic, since in addition to defects in the synthesis of EPS, lipopolysaccharide, and/or capsular polysaccharides significant increases in the synthesis and secretion of cyclic beta-(1,2)-glucans were observed. We concluded that it is impossible to correlate a defect in the synthesis of a particular polysaccharide with nodulation characteristics. Images PMID:8423148

  7. Physiology of ex planta nitrogenase activity in Rhizobium japonicum

    SciTech Connect

    Agarwal, A.K.; Keister, D.L.

    1983-05-01

    Thirty-nine wild-type strains of Rhizobium japonicum have been studied for their ability to synthesize nitrogenase ex planta in defined liquid media under microaerobic conditions. Twenty-one produced more than trace amounts of acetylene reduction activity, but only a few of these yielded high activity. The oxygen response curves were similar for most of the nitrogenase-positive strains. The strains derepressible for activity had several phenotypic characteristics different from non-derepressible strains. These included slower growth and lower oxygen consumption under microaerobic conditions and lower extracellular polysaccharide production. Extracellular polysaccharide production during growth on gluconate in every nitrogenase-positive strain assayed was lower under both aerobic and microaerobic conditions than the non-depressible strains. These phenotypic characteristics may be representative of a genotype of a subspecies of R. japonicum. These studies were done in part to enlarge the base number of strains available for studies on the physiology, biochemistry, and genetics of nitrogen fixation. (35 Refs.)

  8. Characterization of swarming motility in Rhizobium leguminosarum bv. viciae.

    PubMed

    Tambalo, Dinah D; Yost, Christopher K; Hynes, Michael F

    2010-06-01

    We have characterized swarming motility in Rhizobium leguminosarum strains 3841 and VF39SM. Swarming was dependent on growth on energy-rich media, and both agar concentration and incubation temperature were critical parameters for surface migration. A cell density-dependent lag period was observed before swarming motility was initiated. Surface migration began 3-5 days after inoculation and a full swarming phenotype was observed 3 weeks after inoculation. The swarming front was preceded by a clear extracellular matrix, from which we failed to detect surfactants. The edge of the swarming front formed by VF39SM was characterized by hyperflagellated cells arranged in rafts, whereas the cells at the point of inoculation were indistinguishable from vegetative cells. Swarmer cells formed by 3841, in contrast, showed a minor increase in flagellation, with each swarmer cell exhibiting an average of three flagellar filaments, compared with an average of two flagella per vegetative cell. Reflective of their hyperflagellation, the VF39SM swarmer cells demonstrated an increased expression of flagellar genes. VF39SM swarmed better than 3841 under all the conditions tested, and the additional flagellation in VF39SM swarm cells may contribute to this difference. Metabolism of the supplemented carbon source appeared to be necessary for surface migration as strains incapable of utilizing the carbon source failed to swarm. We also observed that swarmer cells have increased resistance to several antibiotics. PMID:20455952

  9. Succinate transport by free-living forms of Rhizobium japonicum.

    PubMed Central

    McAllister, C F; Lepo, J E

    1983-01-01

    We have demonstrated that the transport of succinate into the cells of Rhizobium japonicum strains USDA 110 and USDA 217 is severely inhibited by cyanide, azide, and 2,4-dinitrophenol, but not by arsenate. These results suggest an active mechanism of transport that is dependent on an energized membrane, but does not directly utilize ATP. The apparent Km for succinate was 3.8 microM for strain USDA 110 and 1.8 microM for strain USDA 217; maximal transport velocities were 1.5 and 3.3 nmol of succinate per min per mg of protein, respectively. The expression of the succinate uptake activity was inducible rather than constitutive, with succinate and structurally related compounds being the most effective inducers. The mechanism showed some specificity for succinate and similar organic acids; fumarate and L-malate were classical competitive inhibitors of the system. In general, the best competing compounds were also the best carbon substrates for induction of succinate uptake activity. EDTA inhibited the transport of succinate, implying a role for divalent cations in the system. When various divalent cations were used to reconstitute EDTA-inhibited activity, Ca2+ was most effective, followed by Mg2+, which restored activity at about half the efficiency of Ca2+. Growth media that were supplemented with increased Ca2+ concentration supported more rapid growth with succinate as the carbon substrate, and cells from such media showed higher specific activities of succinate transport. PMID:6402487

  10. High catalase production by Rhizobium radiobacter strain 2-1.

    PubMed

    Nakayama, Mami; Nakajima-Kambe, Toshiaki; Katayama, Hideki; Higuchi, Kazuhiko; Kawasaki, Yoshio; Fuji, Ryujiro

    2008-12-01

    To promote the application of catalase for treating wastewater containing hydrogen peroxide, bacteria exhibiting high catalase activity were screened. A bacterium, designated strain 2-1, with high catalase activity was isolated from the wastewater of a beverage factory that uses hydrogen peroxide. Strain 2-1 was identified as Rhizobium radiobacter (formerly known as Agrobacterium tumefaciens) on the basis of both phenotypic and genotypic characterizations. Although some strains of R. radiobacter are known plant pathogens, polymerase chain reaction (PCR) analysis showed that strain 2-1 has no phytopathogenic factor. Compared with a type strain of R. radiobacter, the specific catalase activity of strain 2-1 was approximately 1000-fold. Moreover, Strain 2-1 grew faster and exhibited considerably higher catalase activity than other microorganisms that have been used for industrial catalase production. Strain 2-1 is harmless to humans and the environment and produces catalase efficiently, suggesting that strain 2-1 is a good resource for the mass production of catalase for the treatment of hydrogen peroxide-containing wastewater. PMID:19134550

  11. Root Hair Deformations Associated with Fractionated Extracts from Rhizobium trifolii†

    PubMed Central

    Ervin, Sean E.; Hubbell, David H.

    1985-01-01

    Components from culture fluid and whole cells of Rhizobium trifolii were examined for effects on root hair morphology of white clover seedlings (Trifolium repens var. Ladino). Cell-free culture fluid, exopolysaccharides, supernatant fluid from the precipitation of the exopolysaccharides, capsular polysaccharides, lipopolysaccharides, and a protein fraction from culture fluids were assayed for morphogenetic effects on the root hairs of axenically grown clover seedlings. Crude fractions were chromatographed on Bio Gel A-5m (Bio-Rad Laboratories), and fractions collected were similarly assayed. Hexose, uronic acid, and protein concentrations were determined for all fractions assayed. Gel chromatography indicated the materials with deforming ability to be of high molecular weight (>10,000). For all fractions except exopolysaccharide, deforming ability was associated with a protein component. This suggested that two components were associated with deformation; both contained polysaccharides and one contained protein. Crude fractions differed in their ability to cause deformations and indicated the following relative ability (in decreasing order) to deform root hairs: cell-free culture fluid, capsular polysaccharides, protein from culture fluids, exopolysaccharide, and cell envelope. Lipopolysaccharides had no effect. Images PMID:16346709

  12. Herbivores alter the fitness benefits of a plant-rhizobium mutualism

    NASA Astrophysics Data System (ADS)

    Heath, Katy D.; Lau, Jennifer A.

    2011-03-01

    Mutualisms are best understood from a community perspective, since third-party species have the potential to shift the costs and benefits in interspecific interactions. We manipulated plant genotypes, the presence of rhizobium mutualists, and the presence of a generalist herbivore and assessed the performance of all players in order to test whether antagonists might alter the fitness benefits of plant-rhizobium mutualism, and vice versa how mutualists might alter the fitness consequences of plant-herbivore antagonism. We found that plants in our experiment formed more associations with rhizobia (root nodules) in the presence of herbivores, thereby increasing the fitness benefits of mutualism for rhizobia. In contrast, the effects of rhizobia on herbivores were weak. Our data support a community-dependent view of these ecological interactions, and suggest that consideration of the aboveground herbivore community can inform ecological and evolutionary studies of legume-rhizobium interactions.

  13. Synthesis and accumulation of poly(3-hydroxybutyric acid) by Rhizobium sp.

    PubMed

    Manna, A; Pal, S; Paul, A K

    2000-01-01

    Forty-two Rhizobium strains obtained from different culture collections were evaluated quantitatively for poly(3-hydroxy-butyric acid) [PHB] production in shake flask culture. The majority of the strains produced the maximum amount of PHB during the late exponential or stationary phase of growth. Synthesis and accumulation of PHB in different species of Rhizobium were found to vary between 1-38% of their dry biomass. Growth and PHB production by the Rhizobium strain TAL-640 were greatly influenced by the C-source and D-mannitol was fundamental to both processes. The identity and purity of PHB isolated from TAL-640 have also been confirmed by UV-, IR- and 1H-NMR spectroscopic analyses. PMID:10866363

  14. Different metabolic features of Bacteroides fragilis growing in the presence of glucose and exopolysaccharides of bifidobacteria

    PubMed Central

    Rios-Covian, David; Sánchez, Borja; Salazar, Nuria; Martínez, Noelia; Redruello, Begoña; Gueimonde, Miguel; de los Reyes-Gavilán, Clara G.

    2015-01-01

    Bacteroides is among the most abundant microorganism inhabiting the human intestine. They are saccharolytic bacteria able to use dietary or host-derived glycans as energy sources. Some Bacteroides fragilis strains contribute to the maturation of the immune system but it is also an opportunistic pathogen. The intestine is the habitat of most Bifidobacterium species, some of whose strains are considered probiotics. Bifidobacteria can synthesize exopolysaccharides (EPSs), which are complex carbohydrates that may be available in the intestinal environment. We studied the metabolism of B. fragilis when an EPS preparation from bifidobacteria was added to the growth medium compared to its behavior with added glucose. 2D-DIGE coupled with the identification by MALDI-TOF/TOF evidenced proteins that were differentially produced when EPS was added. The results were supported by RT-qPCR gene expression analysis. The intracellular and extracellular pattern of certain amino acids, the redox balance and the α-glucosidase activity were differently affected in EPS with respect to glucose. These results allowed us to hypothesize that three general main events, namely the activation of amino acids catabolism, enhancement of the transketolase reaction from the pentose-phosphate cycle, and activation of the succinate-propionate pathway, promote a shift of bacterial metabolism rendering more reducing power and optimizing the energetic yield in the form of ATP when Bacteroides grow with added EPSs. Our results expand the knowledge about the capacity of B. fragilis for adapting to complex carbohydrates and amino acids present in the intestinal environment. PMID:26347720

  15. Different metabolic features of Bacteroides fragilis growing in the presence of glucose and exopolysaccharides of bifidobacteria.

    PubMed

    Rios-Covian, David; Sánchez, Borja; Salazar, Nuria; Martínez, Noelia; Redruello, Begoña; Gueimonde, Miguel; de Los Reyes-Gavilán, Clara G

    2015-01-01

    Bacteroides is among the most abundant microorganism inhabiting the human intestine. They are saccharolytic bacteria able to use dietary or host-derived glycans as energy sources. Some Bacteroides fragilis strains contribute to the maturation of the immune system but it is also an opportunistic pathogen. The intestine is the habitat of most Bifidobacterium species, some of whose strains are considered probiotics. Bifidobacteria can synthesize exopolysaccharides (EPSs), which are complex carbohydrates that may be available in the intestinal environment. We studied the metabolism of B. fragilis when an EPS preparation from bifidobacteria was added to the growth medium compared to its behavior with added glucose. 2D-DIGE coupled with the identification by MALDI-TOF/TOF evidenced proteins that were differentially produced when EPS was added. The results were supported by RT-qPCR gene expression analysis. The intracellular and extracellular pattern of certain amino acids, the redox balance and the α-glucosidase activity were differently affected in EPS with respect to glucose. These results allowed us to hypothesize that three general main events, namely the activation of amino acids catabolism, enhancement of the transketolase reaction from the pentose-phosphate cycle, and activation of the succinate-propionate pathway, promote a shift of bacterial metabolism rendering more reducing power and optimizing the energetic yield in the form of ATP when Bacteroides grow with added EPSs. Our results expand the knowledge about the capacity of B. fragilis for adapting to complex carbohydrates and amino acids present in the intestinal environment. PMID:26347720

  16. Biochemical and serological characterization of Bacteroides intermedius strains isolated from the deep periodontal pocket.

    PubMed Central

    Dahlén, G; Wikström, M; Renvert, S; Gmür, R; Guggenheim, B

    1990-01-01

    Fifty-one fluorescence-positive black-pigmented Bacteroides strains obtained from 51 patients with deep periodontal pockets (greater than 6 mm) were identified and characterized. Fifty of these strains were presumptively identified as Bacteroides intermedius according to the indole reaction. This was confirmed by further biochemical characterization. The 50 strains from diseased sites were then compared with 16 B. intermedius strains isolated from periodontally healthy individuals with no signs of destructive periodontal disease. Tests for antimicrobial susceptibility showed similar patterns for all 50 pocket-derived strains, except for one beta-lactamase-positive strain that was resistant to penicillin G and ampicillin. Forty-seven strains were tested for binding of three monoclonal antibodies defining three distinct serogroups of B. intermedius. Thirty-one strains belonged to serogroup I, three to serogroup II and thirteen to serogroup III. In comparison to the strains from the shallow periodontal pockets, serogroup I was significantly overrepresented in the patient group with periodontal disease. We conclude that saccharolytic black-pigmented Bacteroides species from deep periodontal pockets constituted, with very rare exceptions, a biochemically homogeneous but antigenically heterogeneous group of B. intermedius and that serogroup I is predominantly found in deep periodontal lesions. PMID:2229351

  17. Role of nickel in membrane-bound hydrogenase and nickel metabolism in Rhizobium japonicum

    SciTech Connect

    Stults, L.W.

    1986-01-01

    The membrane-bound hydrogenase of Rhizobium japonicum requires nickel for activity. Radioactive /sup 63/Ni co-migrates with hydrogenase activity in native gel systems and co-elutes with purified hydrogenase form an affinity matrix column. A simplified scheme for the purification of hydrogenase has been developed and constitutes the first report of the aerobic purification of this enzyme from R. japonicum. The aerobic purification utilizes the general affinity matrix. Reactive Red 120-agarose and results in higher specific activity and yield of enzyme than previously reported. The stability of aerobically purified hydrogenase to oxygen is substantially greater than that reported for anaerobically isolated enzyme. Reduction of the aerobically purified enzyme in the presence of oxygen, however, results in the rapid loss of activity. R. japonicum cells accumulate nickel during heterotrophic growth and as non-growing cells. The hydrogenase constitutive mutant SR470 accumulates substantially greater amounts of nickel under both conditions. Kinetic studies indicate that the nickel uptake system in the hydrogenase constitutive mutant SR470 is upregulated relative to SRwt cells. The uptake system is specific for nickel, although a 10-fold excess (relative to nickel) of copper or zinc inhibits nickel uptake. The nickel uptake system appears to require energy. Under nickel-free conditions hydrogenase protein is not synthesized as determined by cross-reactivity with antibodies directed against hydrogenase, indicating that nickel regulates the formation of the enzyme as well as being a constituent of the active protein.

  18. Genetic Locus Required for Antigenic Maturation of Rhizobium etli CE3 Lipopolysaccharide

    PubMed Central

    Duelli, Dominik M.; Tobin, Andrea; Box, Jodie M.; Kolli, V. S. Kumar; Carlson, Russell W.; Noel, K. Dale

    2001-01-01

    Rhizobium etli modifies lipopolysaccharide (LPS) structure in response to environmental signals, such as low pH and anthocyanins. These LPS modifications result in the loss of reactivity with certain monoclonal antibodies. The same antibodies fail to recognize previously isolated R. etli mutant strain CE367, even in the absence of such environmental cues. Chemical analysis of the LPS in strain CE367 demonstrated that it lacked the terminal sugar of the wild-type O antigen, 2,3,4-tri-O-methylfucose. A 3-kb stretch of DNA, designated as lpe3, restored wild-type antigenicity when transferred into CE367. From the sequence of this DNA, five open reading frames were postulated. Site-directed mutagenesis and complementation analysis suggested that the genes were organized in at least two transcriptional units, both of which were required for the production of LPS reactive with the diagnostic antibodies. Growth in anthocyanins or at low pH did not alter the specific expression of gusA from the transposon insertion of mutant CE367, nor did the presence of multiple copies of lpe3 situated behind a strong, constitutive promoter prevent epitope changes induced by these environmental cues. Mutations of the lpe genes did not prevent normal nodule development on Phaseolus vulgaris and had very little effect on the occupation of nodules in competition with the wild-type strain. PMID:11567006

  19. The rkpGHI and -J genes are involved in capsular polysaccharide production by Rhizobium meliloti.

    PubMed Central

    Kiss, E; Reuhs, B L; Kim, J S; Kereszt, A; Petrovics, G; Putnoky, P; Dusha, I; Carlson, R W; Kondorosi, A

    1997-01-01

    The first complementation unit of the fix-23 region of Rhizobium meliloti, which comprises six genes (rkpAB-CDEF) exhibiting similarity to fatty acid synthase genes, is required for the production of a novel type of capsular polysaccharide that is involved in root nodule development and structurally analogous to group II K antigens found in Escherichia coli (G. Petrovics, P. Putnoky, R. Reuhs, J. Kim, T. A. Thorp, K. D. Noel, R. W. Carlson, and A. Kondorosi, Mol. Microbiol. 8:1083-1094, 1993; B. L. Reuhs, R. W. Carlson, and J. S. Kim, J. Bacteriol. 175:3570-3580, 1993). Here we present the nucleotide sequence for the other three complementation units of the fix-23 locus, revealing the presence of four additional open reading frames assigned to genes rkpGHI and -J. The putative RkpG protein shares similarity with acyltransferases, RkpH is homologous to short-chain alcohol dehydrogenases, and RkpJ shows significant sequence identity with bacterial polysaccharide transport proteins, such as KpsS of E. coli. No significant homology was found for RkpI. Biochemical and immunological analysis of Tn5 derivatives for each gene demonstrated partial or complete loss of capsular polysaccharides from the cell surface; on this basis, we suggest that all genes in the fix-23 region are required for K-antigen synthesis or transport. PMID:9079896

  20. Assignment of symbiotic developmental phenotypes to common and specific nodulation (nod) genetic loci of Rhizobium meliloti.

    PubMed Central

    Debellé, F; Rosenberg, C; Vasse, J; Maillet, F; Martinez, E; Dénarié, J; Truchet, G

    1986-01-01

    Rhizobium meliloti nodulation (nod) genes required for specific infection and nodulation of alfalfa have been cloned. Transposon Tn5 mutagenesis defined three nod regions spanning 16 kilobases of the pSym megaplasmid. Genetic and cytological studies of 62 nodulation-defective mutants allowed the assignment of symbiotic developmental phenotypes to common and specific nod loci. Root hair curling was determined by both common (region I) and specific (region III) nod transcription units; locus IIIb (nodH gene) positively controlled curling on the homologous host alfalfa, whereas loci IIIa (nodFE) and IIIb (nodH) negatively controlled curling on heterologous hosts. Region I (nodABC) was required for bacterial penetration and infection thread initiation in shepherd's crooks, and the nodFE transcription unit controlled infection thread development within the alfalfa root hair. In contrast, induction of nodule organogenesis, which can be triggered from a distance, seemed to be controlled by common nodABC genes and not to require specific nod genes nodFE and nodH. Region II affected the efficiency of hair curling and infection thread formation. Images PMID:3023297

  1. Characterization of Rhizobium grahamii extrachromosomal replicons and their transfer among rhizobia

    PubMed Central

    2014-01-01

    Background Rhizobium grahamii belongs to a new phylogenetic group of rhizobia together with Rhizobium mesoamericanum and other species. R. grahamii has a broad-host-range that includes Leucaena leucocephala and Phaseolus vulgaris, although it is a poor competitor for P. vulgaris nodulation in the presence of Rhizobium etli or Rhizobium phaseoli strains. This work analyzed the genome sequence and transfer properties of R. grahamii plasmids. Results Genome sequence was obtained from R. grahamii CCGE502 type strain isolated from Dalea leporina in Mexico. The CCGE502 genome comprises one chromosome and two extrachromosomal replicons (ERs), pRgrCCGE502a and pRgrCCGE502b. Additionally, a plasmid integrated in the CCGE502 chromosome was found. The genomic comparison of ERs from this group showed that gene content is more variable than average nucleotide identity (ANI). Well conserved nod and nif genes were found in R. grahamii and R. mesoamericanum with some differences. R. phaseoli Ch24-10 genes expressed in bacterial cells in roots were found to be conserved in pRgrCCGE502b. Regarding conjugative transfer we were unable to transfer the R. grahamii CCGE502 symbiotic plasmid and its megaplasmid to other rhizobial hosts but we could transfer the symbiotic plasmid to Agrobacterium tumefaciens with transfer dependent on homoserine lactones. Conclusion Variable degrees of nucleotide identity and gene content conservation were found among the different R. grahamii CCGE502 replicons in comparison to R. mesoamericanum genomes. The extrachromosomal replicons from R. grahamii were more similar to those found in phylogenetically related Rhizobium species. However, limited similarities of R. grahamii CCGE502 symbiotic plasmid and megaplasmid were observed in other more distant Rhizobium species. The set of conserved genes in R. grahamii comprises some of those that are highly expressed in R. phaseoli on plant roots, suggesting that they play an important role in root colonization

  2. Rhizobium acidisoli sp. nov., isolated from root nodules of Phaseolus vulgaris in acid soils.

    PubMed

    Román-Ponce, Brenda; Jing Zhang, Yu; Soledad Vásquez-Murrieta, María; Hua Sui, Xin; Feng Chen, Wen; Carlos Alberto Padilla, Juan; Wu Guo, Xian; Lian Gao, Jun; Yan, Jun; Hong Wei, Ge; Tao Wang, En

    2016-01-01

    Two Gram-negative, aerobic, non-motile, rod-shaped bacterial strains, FH13T and FH23, representing a novel group of Rhizobium isolated from root nodules of Phaseolus vulgaris in Mexico, were studied by a polyphasic analysis. Phylogeny of 16S rRNA gene sequences revealed them to be members of the genus Rhizobium related most closely to 'Rhizobium anhuiense' CCBAU 23252 (99.7 % similarity), Rhizobium leguminosarum USDA 2370T (98.6 %), and Rhizobium sophorae CCBAU 03386T and others ( ≤ 98.3 %). In sequence analyses of the housekeeping genes recA, glnII and atpD, both strains formed a subclade distinct from all defined species of the genus Rhizobium at sequence similarities of 82.3-94.0 %, demonstrating that they represented a novel genomic species in the genus Rhizobium. Mean levels of DNA-DNA relatedness between the reference strain FH13T and the type strains of related species varied between 13.0 ± 2.0 and 52.1 ± 1.2 %. The DNA G+C content of strain FH13T was 63.5 mol% (Tm). The major cellular fatty acids were 16 : 0, 17 : 0 anteiso, 18 : 0, summed feature 2 (12 : 0 aldehyde/unknown 10.928) and summed feature 8 (18 : 1ω7c). The fatty acid 17 : 1ω5c was unique for this strain. Some phenotypic features, such as failure to utilize adonitol, l-arabinose, d-fructose and d-fucose, and ability to utilize d-galacturonic acid and itaconic acid as carbon source, could also be used to distinguish strain FH13T from the type strains of related species. Based upon these results, a novel species, Rhizobium acidisoli sp. nov., is proposed, with FH13T ( = CCBAU 101094T = HAMBI 3626T = LMG 28672T) as the type strain. PMID:26530784

  3. Specific Detection of Bradyrhizobium and Rhizobium Strains Colonizing Rice (Oryza sativa) Roots by 16S-23S Ribosomal DNA Intergenic Spacer-Targeted PCR

    PubMed Central

    Tan, Zhiyuan; Hurek, Thomas; Vinuesa, Pablo; Müller, Peter; Ladha, Jagdish K.; Reinhold-Hurek, Barbara

    2001-01-01

    In addition to forming symbiotic nodules on legumes, rhizobial strains are members of soil or rhizosphere communities or occur as endophytes, e.g., in rice. Two rhizobial strains which have been isolated from root nodules of the aquatic legumes Aeschynomene fluminensis (IRBG271) and Sesbania aculeata (IRBG74) were previously found to promote rice growth. In addition to analyzing their phylogenetic positions, we assessed the suitability of the 16S-23S ribosomal DNA (rDNA) intergenic spacer (IGS) sequences for the differentiation of closely related rhizobial taxa and for the development of PCR protocols allowing the specific detection of strains in the environment. 16S rDNA sequence analysis (sequence identity, 99%) and phylogenetic analysis of IGS sequences showed that strain IRBG271 was related to but distinct from Bradyrhizobium elkanii. Rhizobium sp. (Sesbania) strain IRBG74 was located in the Rhizobium-Agrobacterium cluster as a novel lineage according to phylogenetic 16S rDNA analysis (96.8 to 98.9% sequence identity with Agrobacterium tumefaciens; emended name, Rhizobium radiobacter). Strain IRBG74 harbored four copies of rRNA operons whose IGS sequences varied only slightly (2 to 9 nucleotides). The IGS sequence analyses allowed intraspecies differentiation, especially in the genus Bradyrhizobium, as illustrated here for strains of Bradyrhizobium japonicum, B. elkanii, Bradyrhizobium liaoningense, and Bradyrhizobium sp. (Chamaecytisus) strain BTA-1. It also clearly differentiated fast-growing rhizobial species and strains, albeit with lower statistical significance. Moreover, the high sequence variability allowed the development of highly specific IGS-targeted nested-PCR assays. Strains IRBG74 and IRBG271 were specifically detected in complex DNA mixtures of numerous related bacteria and in the DNA of roots of gnotobiotically cultured or even of soil-grown rice plants after inoculation. Thus, IGS sequence analysis is an attractive technique for both microbial

  4. Efficient and regioselective synthesis of globotriose by a novel α-galactosidase from Bacteroides fragilis.

    PubMed

    Gong, Wei; Xu, Li; Gu, Guofeng; Lu, Lili; Xiao, Min

    2016-08-01

    Globotriose (Galα1-4Galβ1-4Glc) is an important cell surface epitope that acts as the receptor for Shiga-like toxins, and it is also the core structure of Globo H and SSEA4 that are tumor-associated glycans. Hence, the enzymatic synthesis of globotriose would be necessary for the development of carbohydrate-based therapeutics for bacterial infections and cancers. Here, a novel GH27 α-galactosidase gene (agaBf3S), a 1521-bp DNA encoding 506 amino acids with a calculated molecular mass of 57.7 kDa, from Bacteroides fragilis NCTC9343 was cloned and heterogeneously expressed in Escherichia coli. The recombinant enzyme AgaBf3S preferentially hydrolyzed p-nitrophenyl-α-D-galactopyranoside (pNPαGal) in all tested nitrophenyl glycosides. It showed maximum activity at pH 4.5 and 40 °C, and it was stable at pH 4.0-11.0 below 40 °C and metal-independent. The K m and k cat values for pNPαGal, melibiose, and globotriose were 1.27 mM and 172.97 S(-1), 62.76 mM and 17.74 S(-1), and 4.62 mM and 388.45 S(-1), respectively. AgaBf3S could transfer galactosyl residue from pNPαGal to lactose (Galβ1-4Glc) with high efficiency and strict α1-4 regioselectivity. The effects of initial substrate concentration, pH, temperature, and reaction time on transglycosylation reaction catalyzed by AgaBf3S were studied in detail. AgaBf3S could synthesize globotriose as a single transglycosylation product with a maximum yield of 32.4 % from 20 mM pNPαGal and 500 mM lactose (pH 4.5) at 40 °C for 30 min. This new one-enzyme one-step synthetic reaction is simple, fast, and low cost, which provides a promising alternative to the current synthetic methods for access to pharmaceutically important Galα1-4-linked oligosaccharides. PMID:27020280

  5. Enhanced Symbiotic Performance by Rhizobium tropici Glycogen Synthase Mutants

    PubMed Central

    Marroquí, Silvia; Zorreguieta, Angeles; Santamaría, Carmen; Temprano, Francisco; Soberón, Mario; Megías, Manuel; Downie, J. Allan

    2001-01-01

    We isolated a Tn5-induced Rhizobium tropici mutant that has enhanced capacity to oxidize N,N-dimethyl-p-phenylendiamine (DMPD) and therefore has enhanced respiration via cytochrome oxidase. The mutant had increased levels of the cytochromes c1 and CycM and a small increase in the amount of cytochrome aa3. In plant tests, the mutant increased the dry weight of Phaseolus vulgaris plants by 20 to 38% compared with the control strain, thus showing significantly enhanced symbiotic performance. The predicted product of the mutated gene is homologous to glycogen synthases from several bacteria, and the mutant lacked glycogen. The DNA sequence of the adjacent gene region revealed six genes predicted to encode products homologous to the following gene products from Escherichia coli: glycogen phosphorylase (glgP), glycogen branching enzyme (glgB), ADP glucose pyrophosphorylase (glgC), glycogen synthase (glgA), phosphoglucomutase (pgm), and glycogen debranching enzyme (glgX). All six genes are transcribed in the same direction, and analysis with lacZ gene fusions suggests that the first five genes are organized in one operon, although pgm appears to have an additional promoter; glgX is transcribed independently. Surprisingly, the glgA mutant had decreased levels of high-molecular-weight exopolysaccharide after growth on glucose, but levels were normal after growth on galactose. A deletion mutant was constructed in order to generate a nonpolar mutation in glgA. This mutant had a phenotype similar to that of the Tn5 mutant, indicating that the enhanced respiration and symbiotic nitrogen fixation and decreased exopolysaccharide were due to mutation of glgA and not to a polar effect on a downstream gene. PMID:11208782

  6. Autecology in Rhizospheres and Nodulating Behavior of Indigenous Rhizobium trifolii†

    PubMed Central

    Demezas, David H.; Bottomley, Peter J.

    1986-01-01

    Indigenous serotype 1-01 of Rhizobium trifolii occupied significantly fewer nodules (6%) on plants of soil-grown noninoculated subterranean clover (Trifolium subterraneum L.) cv. Woogenellup than on cv. Mt. Barker (36%) sampled at the flowering stage of growth. Occupancy by indigenous serotype 2-01, was not significantly different on the two cultivars (16 and 26%). Serotype-specific, fluorescent-antibody conjugates were synthesized and used to enumerate the indigenous serotypes in host (clovers) and nonhost (annual rye-grass, Lolium multiflorum L.) rhizospheres and in nonplanted soil. The form and concentration of Ca2+ in the flocculating mixture and the presence of phosphate anions in the extracting solution were both critical for enumerating R. trifolii in Whobrey soil. The two serotypes were present in similar numbers in nonplanted soil (ca. 106 per g of soil) and each represented ca. 10% of the total R. trifolii population. Although host rhizospheres did not preferentially stimulate either serotype, the mean population densities of serotype 2-01 were significantly greater (P = 0.05) than those of serotype 1-01 in clover rhizospheres on 8 of 14 samplings made between the time of seeding and the appearance of nodules (day 12). In this experiment, and in contrast to our earlier findings, serotype 1-01 occupied significantly fewer (P ≤ 0.05) of the nodules (7 to 16%) on both cultivars than serotype 2-01 (51%) when sampled at 4 weeks. Differences between cultivars became apparent as the plants matured. There was a threefold increase (7 to 21%) in nodules occupied by serotype 1-01 on cv. Mt. Barker between 4 and 16 weeks. This was accompanied by increases in nodules coinhabited by both nonidentifiable occupants and either serotype 1-01 (0 to 20%) or 2-01 (11 to 51%). No increases in either of these parameters were observed on cv. Woogenellup. PMID:16347198

  7. Response of Andean and Mesoamerican common bean genotypes to inoculation with rhizobium strains.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In most common bean (Phaseolus vulgaris L.) production regions of Latin America, inoculants are rarely used by farmers in spite of several studies that demonstrate the importance of Rhizobium inoculation on commercial production of legume crops. This study investigated specific bean host plant-Rhizo...

  8. Preservation of Rhizobium viability and symbiotic infectivity by suspension in water

    SciTech Connect

    Crist, D.K.; Wyza, R.E.; Mills, K.K.; Bauer, W.D.; Evans, W.R.

    1984-05-01

    Three Rhizobium japonicum strains and two slow-growing cowpea-type Rhizobium strains were found to remain viable and able to rapidly nodulate their respective hosts after being stored in purified water at ambient temperatures for periods of 1 year and longer. Three fast-growing Rhizobium species did not remain viable under the same water storage conditions. After dilution of slow-growing Rhizobium strains with water to 10/sup 3/ to 10/sup 5/ cells ml/sup -1/, the bacteria multiplied until the viable cell count reached levels of between 10/sub 6/ and 10/sup 7/ cells ml/sup -1/. The viable cell count subsequently remained fairly constant. When the rhizobia were diluted to 10/sup 7/ cells ml/sup -1/, they did not multiply, but full viability was maintained. If the rhizobia were washed and suspended at 10/sup 9/ cells ml/sup -1/, viability slowly declined to 10/sup 7/ cells ml/sup -1/ during 9 months of storage. Scanning electron microscopy showed that no major morphological changes took place during storage. Preservation of slow-growing rhizobia in water suspensions could provide a simple and inexpensive alternative to current methods for the preservation of rhizobia for legume inoculation. 25 references, 7 figures, 2 tables.

  9. Beta-2-linked glucans secreted by fast-growing species of Rhizobium

    SciTech Connect

    York, W.S.; McNeil, M.; Darvill, A.G.; Albersheim, P.

    1980-04-01

    Fast-growing species of Rhizobium were found to secrete low-molecular-weight ..beta..-2-linked glucans when cultured in synthetic liquid medium. These glucans are quite similar to ..beta..-2-linked glucans produced by species of Agrobacterium. No reducing terminus was detected in these glucans.

  10. Accumulation of Amino Acids in Rhizobium sp. Strain WR1001 in Response to Sodium Chloride Salinity

    PubMed Central

    Hua, Sui-Sheng T.; Tsai, Victor Y.; Lichens, Georgia M.; Noma, Amy T.

    1982-01-01

    Rhizobium sp. strain WR1001, isolated from the Sonoran Desert by Eskew and Ting, was found to be able to grow in defined medium containing NaCl up to 500 mM, a concentration approaching that of sea water. Therefore, it is a valuable strain for studying the biochemical basis of salt tolerance. Intracellular free glutamate was found to increase rapidly in response to osmotic stress by NaCl. It accounted for 88% of the amino acid pool when the bacterium was grown in 500 mM NaCl. The role of glutamate dehydrogenase in glutamate biosynthesis was examined in several Rhizobium strains. Both NADH- and NADPH-dependent glutamate dehydrogenase activities in various Rhizobium strains were observed. The range of activity differed considerably depending on the particular strain. KCl (500 mM) did not stimulate glutamate dehydrogenase activity, as reported in a number of bacterial strains by Measures. The low activity of glutamate dehydrogenase in Rhizobium sp. strain WR1001 apparently cannot fulfill a biosynthetic function of glutamate formation in response to medium NaCl concentrations. PMID:16346049

  11. Beta-2-linked glucans secreted by fast-growing species of Rhizobium.

    PubMed Central

    York, W S; McNeil, M; Darvill, A G; Albersheim, P

    1980-01-01

    Fast-growing species of Rhizobium were found to secrete low-molecular-weight beta-2-linked glucans when cultured in synthetic liquid medium. These glucans are quite similar to beta-2-linked glucans produced by species of Agrobacterium. No reducing terminus was detected in these glucans. PMID:7372570

  12. Rhizobium anhuiense sp. nov., isolated from effective nodules of Vicia faba and Pisum sativum.

    PubMed

    Zhang, Yu Jing; Zheng, Wen Tao; Everall, Isobel; Young, J Peter W; Zhang, Xiao Xia; Tian, Chang Fu; Sui, Xin Hua; Wang, En Tao; Chen, Wen Xin

    2015-09-01

    Four rhizobia-like strains, isolated from root nodules of Pisum sativum and Vicia faba grown in Anhui and Jiangxi Provinces of China, were grouped into the genus Rhizobium but were distinct from all recognized species of the genus Rhizobium by phylogenetic analysis of 16S rRNA and housekeeping genes. The combined sequences of the housekeeping genes atpD, recA and glnII for strain CCBAU 23252(T) showed 86.9 to 95% similarity to those of known species of the genus Rhizobium. All four strains had nodC and nifH genes and could form effective nodules with Pisum sativum and Vicia faba, and ineffective nodules with Phaseolus vulgaris, but did not nodulate Glycine max, Arachis hypogaea, Medicago sativa, Trifolium repens or Lablab purpureus in cross-nodulation tests. Fatty acid composition, DNA-DNA relatedness and a series of phenotypic tests also separated these strains from members of closely related species. Based on all the evidence, we propose a novel species, Rhizobium anhuiense sp. nov., and designate CCBAU 23252(T) ( = CGMCC 1.12621(T) = LMG 27729(T)) as the type strain. This strain was isolated from a root nodule of Vicia faba and has a DNA G+C content of 61.1 mol% (Tm). PMID:26025940

  13. Genome of Rhizobium sp. UR51a, Isolated from Rice Cropped in Southern Brazilian Fields.

    PubMed

    de Souza, Rocheli; Sant'Anna, Fernando Hayashi; Ambrosini, Adriana; Tadra-Sfeir, Michele; Faoro, Helisson; Pedrosa, Fabio Oliveira; Souza, Emanuel Maltempi; Passaglia, Luciane M P

    2015-01-01

    Rhizobium sp. UR51a is a Gram-negative bacterium isolated from roots of rice plants, and it presents plant growth-promoting abilities. The nutrient uptake in rice plants inoculated with UR51a was satisfactory. The genome of strain UR51a is composed of 5,233,443-bp and harbors 5,079 coding sequences. PMID:25838497

  14. Genome of Rhizobium sp. UR51a, Isolated from Rice Cropped in Southern Brazilian Fields

    PubMed Central

    de Souza, Rocheli; Sant’Anna, Fernando Hayashi; Ambrosini, Adriana; Tadra-Sfeir, Michele; Faoro, Helisson; Pedrosa, Fabio Oliveira; Souza, Emanuel Maltempi

    2015-01-01

    Rhizobium sp. UR51a is a Gram-negative bacterium isolated from roots of rice plants, and it presents plant growth-promoting abilities. The nutrient uptake in rice plants inoculated with UR51a was satisfactory. The genome of strain UR51a is composed of 5,233,443-bp and harbors 5,079 coding sequences. PMID:25838497

  15. Rhizobium selenireducens sp. nov. Validation and inclusion onto the list of organisms with standing in nomenclature.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This is a submission to the list of microorganisms with standing in nomenclature. The list of valid microbial names is maintained by the International Journal of Systematic and Evolutionary Microbiology and we are proposing that Rhizobium selenireducens sp. nov. be added to the list as a valid spec...

  16. Nodulation of Sesbania Species by Rhizobium (Agrobacterium) Strain IRBG74 and Other Rhizobia

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Concatenated sequence analysis with 16S rRNA, rpoB and fusA genes identified a strain (IRBG74) isolated from root nodules of the aquatic legume Sesbania cannabina as a close relative of the plant pathogen Rhizobium radiobacter (syn. Agrobacterium tumefaciens). However, DNA:DNA hybridisation with R. ...

  17. [Construction of the gene library of symbiotic nitrogen-fixing Rhizobium lupini].

    PubMed

    Ivanushkin, A G; Marchenko, G N; Chistoserdov, A Iu; Pushkin, A V; Kretovich, V L

    1990-01-01

    The gene bank of the symbiotic nitrogen-fixing bacterium Rhizobium lupini (effective strain 359a) was constructed on plasmid pAYC31 that was used to transform Escherichia coli C6000. The bank contains 6600 clones. Restriction analysis showed that the size of the mean insertion fragment in the plasmid in 6.5 kb. PMID:2190206

  18. Three Cases of Post-Cataract Surgery Endophthalmitis Due to Rhizobium (Agrobacterium) radiobacter

    PubMed Central

    Moreau-Gaudry, Viviane; Chiquet, Christophe; Boisset, Sandrine; Croize, Jacques; Benito, Yvonne; Cornut, Pierre Loïc; Bron, Alain; Vandenesch, François

    2012-01-01

    We present three unrelated post-cataract surgery endophthalmitis cases caused by Rhizobium radiobacter, hospitalized in three different hospitals. Early diagnosis was obtained in two cases by bacterial DNA detection in vitreous samples. All patients recovered from infection, but pars plana vitrectomy was needed in two patients due to rapid clinical deterioration. PMID:22259203

  19. Three cases of post-cataract surgery endophthalmitis due to Rhizobium (Agrobacterium) radiobacter.

    PubMed

    Moreau-Gaudry, Viviane; Chiquet, Christophe; Boisset, Sandrine; Croize, Jacques; Benito, Yvonne; Cornut, Pierre Loïc; Bron, Alain; Vandenesch, François; Maurin, Max

    2012-04-01

    We present three unrelated post-cataract surgery endophthalmitis cases caused by Rhizobium radiobacter, hospitalized in three different hospitals. Early diagnosis was obtained in two cases by bacterial DNA detection in vitreous samples. All patients recovered from infection, but pars plana vitrectomy was needed in two patients due to rapid clinical deterioration. PMID:22259203

  20. The structure of legume–rhizobium interaction networks and their response to tree invasions

    PubMed Central

    Le Roux, Johannes J.; Mavengere, Natasha R.; Ellis, Allan G.

    2016-01-01

    Establishing mutualistic interactions in novel environments is important for the successful establishment of some non-native plant species. These associations may, in turn, impact native species interaction networks as non-natives become dominant in their new environments. Using phylogenetic and ecological interaction network approaches we provide the first report of the structure of belowground legume–rhizobium interaction networks and how they change along a gradient of invasion (uninvaded, semi invaded and heavily invaded sites) by Australian Acacia species in South Africa’s Cape Floristic Region. We found that native and invasive legumes interact with distinct rhizobial lineages, most likely due to phylogenetic uniqueness of native and invasive host plants. Moreover, legume–rhizobium interaction networks are not nested, but significantly modular with high levels of specialization possibly as a result of legume–rhizobium co-evolution. Although network topology remained constant across the invasion gradient, composition of bacterial communities associated with native legumes changed dramatically as acacias increasingly dominated the landscape. In stark contrast to aboveground interaction networks (e.g. pollination and seed dispersal) we show that invasive legumes do not infiltrate existing native legume–rhizobium networks but rather form novel modules. This absence of mutualist overlap between native and invasive legumes suggests the importance of co-invading rhizobium–acacia species complexes for Acacia invasion success, and argues against a ubiquitous role for the formation and evolutionary refinement of novel interactions. PMID:27255514

  1. Interactions between Bifidobacterium and Bacteroides Species in Cofermentations Are Affected by Carbon Sources, Including Exopolysaccharides Produced by Bifidobacteria

    PubMed Central

    Rios-Covian, David; Arboleya, Silvia; Hernandez-Barranco, Ana M.; Alvarez-Buylla, Jorge R.; Ruas-Madiedo, Patricia; Gueimonde, Miguel

    2013-01-01

    Cocultures of strains from two Bifidobacterium and two Bacteroides species were performed with exopolysaccharides (EPS) previously purified from bifidobacteria, with inulin, or with glucose as the carbon source. Bifidobacterium longum NB667 and Bifidobacterium breve IPLA20004 grew in glucose but showed poor or no growth in complex carbohydrates (inulin, EPS E44, and EPS R1), whereas Bacteroides grew well in the four carbon sources tested. In the presence of glucose, the growth of Bacteroides thetaiotaomicron DSM-2079 was inhibited by B. breve, whereas it remained unaffected in the presence of B. longum. Ba. fragilis DSM-2151 contributed to a greater survival of B. longum, promoting changes in the synthesis of short-chain fatty acids (SCFA) and organic acids in coculture with respect to monocultures. In complex carbohydrates, cocultures of bifidobacterium strains with Ba. thetaiotaomicron did not modify the behavior of Bacteroides nor improve the poor growth of bifidobacteria. The metabolic activity of Ba. fragilis in coculture with bifidobacteria was not affected by EPS, but greater survival of bifidobacteria at late stages of incubation occurred in cocultures than in monocultures, leading to a higher production of acetic acid than in monocultures. Therefore, cocultures of Bifidobacterium and Bacteroides can behave differently against fermentable carbohydrates as a function of the specific characteristics of the strains from each species. These results stress the importance of considering specific species and strain interactions and not simply higher taxonomic divisions in the relationship among intestinal microbial populations and their different responses to probiotics and prebiotics. PMID:24077708

  2. Interactions between Bifidobacterium and Bacteroides species in cofermentations are affected by carbon sources, including exopolysaccharides produced by bifidobacteria.

    PubMed

    Rios-Covian, David; Arboleya, Silvia; Hernandez-Barranco, Ana M; Alvarez-Buylla, Jorge R; Ruas-Madiedo, Patricia; Gueimonde, Miguel; de los Reyes-Gavilan, Clara G

    2013-12-01

    Cocultures of strains from two Bifidobacterium and two Bacteroides species were performed with exopolysaccharides (EPS) previously purified from bifidobacteria, with inulin, or with glucose as the carbon source. Bifidobacterium longum NB667 and Bifidobacterium breve IPLA20004 grew in glucose but showed poor or no growth in complex carbohydrates (inulin, EPS E44, and EPS R1), whereas Bacteroides grew well in the four carbon sources tested. In the presence of glucose, the growth of Bacteroides thetaiotaomicron DSM-2079 was inhibited by B. breve, whereas it remained unaffected in the presence of B. longum. Ba. fragilis DSM-2151 contributed to a greater survival of B. longum, promoting changes in the synthesis of short-chain fatty acids (SCFA) and organic acids in coculture with respect to monocultures. In complex carbohydrates, cocultures of bifidobacterium strains with Ba. thetaiotaomicron did not modify the behavior of Bacteroides nor improve the poor growth of bifidobacteria. The metabolic activity of Ba. fragilis in coculture with bifidobacteria was not affected by EPS, but greater survival of bifidobacteria at late stages of incubation occurred in cocultures than in monocultures, leading to a higher production of acetic acid than in monocultures. Therefore, cocultures of Bifidobacterium and Bacteroides can behave differently against fermentable carbohydrates as a function of the specific characteristics of the strains from each species. These results stress the importance of considering specific species and strain interactions and not simply higher taxonomic divisions in the relationship among intestinal microbial populations and their different responses to probiotics and prebiotics. PMID:24077708

  3. Rhizobium marinum sp. nov., a malachite-green-tolerant bacterium isolated from seawater.

    PubMed

    Liu, Yang; Wang, Run-Ping; Ren, Chong; Lai, Qi-Liang; Zeng, Run-Ying

    2015-12-01

    A motile, Gram-stain-negative, non-pigmented bacterial strain, designated MGL06T, was isolated from seawater of the South China Sea on selection medium containing 0.1 % (w/v) malachite green. Strain MGL06T showed highest 16S rRNA gene sequence similarity to Rhizobium vignae CCBAU 05176T (97.2 %), and shared 93.2-96.9 % with the type strains of other recognized Rhizobium species. Phylogenetic analyses based on 16S rRNA and housekeeping gene sequences showed that strain MGL06T belonged to the genus Rhizobium. Mean levels of DNA-DNA relatedness between strain MGL06T and R. vignae CCBAU 05176T, Rhizobium huautlense S02T and Rhizobium alkalisoli CCBAU 01393T were 20 ± 3, 18 ± 2 and 14 ± 3 %, respectively, indicating that strain MGL06T was distinct from them genetically. Strain MGL06T did not form nodules on three different legumes, and the nodD and nifH genes were also not detected by PCR or based on the draft genome sequence. Strain MGL06T contained Q-10 as the predominant ubiquinone. The major fatty acid was C18 : 1ω7c/C18 : 1ω6c with minor amounts of C19 : 0 cyclo ω8c, C16 : 0 and C18 : 1ω7c 11-methyl. Polar lipids of strain MGL06T included unknown glycolipids, phosphatidylcholine, aminolipid, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, an unknown polar lipid and aminophospholipid. Based on its phenotypic and genotypic data, strain MGL06T represents a novel species of the genus Rhizobium, for which the name Rhizobium marinum sp. nov. is proposed. The type strain is MGL06T ( = MCCC 1A00836T = JCM 30155T). PMID:26374202

  4. Nodulation gene factors and plant response in the Rhizobium-legume symbiosis. [Nodulation

    SciTech Connect

    Long, S.R.

    1990-01-01

    Our original application aimed to identify genes outside the common nod region involved in nodulation and host range of alfalfa. This has been revised by adding other studies on nodulation gene action and removing molecular studies of gene action. Our restated goals and progress are as follows. An early goal was identification and characterization of additional nodulation genes. By means of transposon mutagenesis, mapping and marker exchange we have established 87 independent mutations in a 20kb area represented by plasmid pRmJT5. We discovered four new genes: nodP, nodD3, syrA and syrM. The sequence, start site and protein product for nodFe, nodG, and nodH were also identified. Regulation of nod FEGH was studied. nod FEGH can be induced by luteolin in the presence of noodle; nodD1; noD3 and syrM, a symbiotic regulator gene also increase transcription of nod FEGH. syrA will interact with syrM; syrM also regulates exopolysaccharide genes and is believed to be a master regulator. As part of these studies, an in vitro transcription/translation system for Rhizobium was developed. Adjacent to nodP we discussed nodQ, nodPQ occurrs in two highly consumed copies. nodQ appears by sequence analysis to be similar to initiation and elongation factors, with the highest homology in the GDP binding domain. We have also investigated the nod strain, WL131. WL131 has an insertion, ISRm3, interrupting nodG, and a nonsase mutation in nodH, nodH is responsible for the lack of nodulation. We are currently investigating supernatant factors, host range effects C by spot inoculation, glucaronidase fusion proteins, and are developing, a single root hair inoculation protocol. 7 refs., 6 figs., 1 tab.

  5. Fermentation of fenugreek fiber, psyllium husk, and wheat bran by Bacteroides ovatus V975.

    PubMed

    Al-Khaldi, S F; Martin, S A; Prakash, L

    1999-10-01

    The objective of this study was to evaluate the ability of the human colonic bacterium Bacteroides ovatus V975 to ferment fenugreek fiber (Fenufibers), psyllium husk (Metamucil), and wheat bran (Wheat Chex). Strain V975 was incubated in basal medium that contained 0.1 g of each fiber source for 0, 24, or 48 h. Little digestion of either fiber source was detected over 48 h, and little acetate or succinate was produced. From the lack of significant fiber digestion and fermentation by B. ovatus, it seems that all three fiber sources could be used as dietary supplements to increase roughage in the human diet. PMID:10486060

  6. Efflux Pump Overexpression in Multiple-Antibiotic-Resistant Mutants of Bacteroides fragilis

    PubMed Central

    Pumbwe, Lilian; Glass, Daniel; Wexler, Hannah M.

    2006-01-01

    Multidrug-resistant mutants of a wild-type Bacteroides fragilis strain (strain ADB77) and a quadruple resistance nodulation division family efflux pump deletion mutant (ADB77 ΔbmeB1 ΔbmeB3 ΔbmeB12 ΔbmeB15) were selected with antimicrobials. Ampicillin, doripenem, imipenem, levofloxacin, and metronidazole selected for mutants from both strains; cefoxitin selected for mutants from strain ADB77 only; and sodium dodecyl sulfate selected mutants from ADB77ΔbmeB1 ΔbmeB3 ΔbmeB12 ΔbmeB15 only. The mutants overexpressed one or more efflux pumps. PMID:16940115

  7. Role of Enterotoxigenic Bacteroides fragilis in Children Less Than 5 Years of Age With Diarrhea in Tabriz, Iran

    PubMed Central

    Akhi, Mohammad Taghi; Jedari Seifi, Sirus; Asgharzadeh, Mohammad; Ahangarzadeh Rezaee, Mohammad; Abdoli Oskuei, Shahram; Pirzadeh, Tahereh; Memar, Mohammad Yousef; Alizadeh, Naser; Seifi Yarijan Sofla, Hasan

    2016-01-01

    Background Diarrhea is the most frequent health problem among children in developing countries. Defining the etiology of acute diarrhea is critical to disease therapy and prevention. Some anaerobic bacteria such as Enterotoxigenic Bacteroides fragilis (ETBF) strains cause diarrheal disease by production of enterotoxin in children less than 5 years old. Objectives This study aimed to evaluate the prevalence of ETBF among common bacteria and viruses causing diarrhea in children aged less than five years. Materials and Methods One hundred diarrheal stools were cultured for detection of aerobic and anaerobic pathogen bacteria by direct plating on selective media and antibiotic susceptibility tests were performed according to clinical and laboratory standards institute (CLSI) guidelines on isolates of ETBF. The enterotoxigenic gene among B. fragilis isolates was also investigated using the polymerase chain reaction (PCR) method. Detection of viral pathogens was carried out using the latex agglutination test. Results Ten B. fragilis were isolated from 100 diarrheal fecal specimens. All isolates were susceptible to metronidazole, while 10% were susceptible to clindamycin. Four (40%) ETBF were isolated. Rotaviruses (57.2%) and adenoviruses (18.6%) were the most frequently detected etiological agents. Conclusions ETBF is one of the etiological agents that may cause diarrhea in children but it is not the commonest of them. Metronidazole is still an effective antibiotic against B. fragilis. Viruses are the most important etiological agents of diarrhea in children less than 5 years of age.

  8. Improved Hybrid Genome Assemblies of Two Strains of Bacteroides xylanisolvens, SD_CC_1b and SD_CC_2a, Obtained Using Illumina and 454 Sequencing Technologies

    PubMed Central

    Ramaraj, Thiruvarangan; Sundararajan, Anitha; Schilkey, Faye D.; DelVecchio, Vito G.; Donlon, Mildred; Ziemer, Cherie

    2014-01-01

    Bacteroides xlyanisolvens strains (SD_CC_1b, SD_CC_2a) isolated from human feces were grown on crystalline cellulose. Cellulolytic properties are not common in Bacteroides species. Here, we report improved genome sequences of both of the B. xlyanisolvens strains. PMID:24699955

  9. Improved hybrid genome assemblies of 2 strains of Bacteroides xylanisolvens SD-CC-1b and SD-CC-2a using Illumina and 454 sequencing technologies

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bacteroides xlyanisolvens strains (SD_CC_1b, SD_CC_2a) isolated from human feces were able to grow on crystalline cellulose. Cellulolytic properties are not common in Bacteroides species. Here, we report improved genome sequences of both the B. xlyanisolvens strains....

  10. Isolation and characterization of Bacteroides host strain HB-73 used to detect sewage specific phages in Hawaii.

    PubMed

    Vijayavel, Kannappan; Fujioka, Roger; Ebdon, James; Taylor, Huw

    2010-06-01

    Previous studies have shown that Escherichia coli and enterococci are unreliable indicators of fecal contamination in Hawaii because of their ability to multiply in environmental soils. In this study, the method of detecting Bacteroides phages as specific markers of sewage contamination in Hawaii's recreational waters was evaluated because these sewage specific phages cannot multiply under environmental conditions. Bacteroides hosts (GB-124, GA-17), were recovered from sewage samples in Europe and were reported to be effective in detecting phages from sewage samples obtained in certain geographical areas. However, GB-124 and GA-17 hosts were ineffective in detecting phages from sewage samples obtained in Hawaii. Bacteroides host HB-73 was isolated from a sewage sample in Hawaii, confirmed as a Bacteroides sp. and shown to recover phages from multiple sources of sewage produced in Hawaii at high concentrations (5.2-7.3 x 10(5) PFU/100 mL). These Bacteroides phages were considered as potential markers of sewage because they also survived for three days in fresh stream water and two days in marine water. Water samples from Hawaii's coastal swimming beaches and harbors, which were known to be contaminated with discharges from streams, were shown to contain moderate (20-187 CFU/100 mL) to elevated (173-816 CFU/100 mL) concentrations of enterococci. These same samples contained undetectable levels (<10 PFU/100 mL) of F+ coliphage and Bacteroides phages and provided evidence to suggest that these enterococci may not necessarily be associated with the presence of raw sewage. These results support previous conclusions that discharges from streams are the major sources of enterococci in coastal waters of Hawaii and the most likely source of these enterococci is from environmental soil rather than from sewage. PMID:20451947

  11. Rhizobium metallidurans sp. nov., a symbiotic heavy metal resistant bacterium isolated from the Anthyllis vulneraria Zn-hyperaccumulator.

    PubMed

    Grison, Claire M; Jackson, Stephen; Merlot, Sylvain; Dobson, Alan; Grison, Claude

    2015-05-01

    A Gram-stain-negative, aerobic, rod-shaped, non-spore-forming bacterium (ChimEc512(T)) was isolated from 56 host seedlings of the hyperaccumulating Anthyllis vulneraria legume, which was on an old zinc mining site at Les Avinières, Saint-Laurent-Le-Minier, Gard, South of France. On the basis of 16S rRNA gene sequence similarities, strain ChimEc512(T) was shown to belong to the genus Rhizobium and to be most closely related to Rhizobium endophyticum CCGE 2052(T) (98.4%), Rhizobium tibeticum CCBAU 85039(T) (98.1%), Rhizobium grahamii CCGE 502(T) (98.0%) and Rhizobium mesoamericanum CCGE 501(T) (98.0%). The phylogenetic relationships of ChimEc512(T) were confirmed by sequencing and analyses of recA and atpD genes. DNA-DNA relatedness values of strain ChimEc512(T) with R. endophyticum CCGE 2052(T), R. tibeticum CCBAU 85039(T), R. mesoamericanum CCGE 52(T), Rhizobium grahamii CCGE 502(T), Rhizobium etli CCBAU 85039(T) and Rhizobium radiobacter KL09-16-8-2(T) were 27, 22, 16, 18, 19 and 11%, respectively. The DNA G+C content of strain ChimEc512(T) was 58.9 mol%. The major cellular fatty acid was C18 : 1ω7c, characteristic of the genus Rhizobium . The polar lipid profile included phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol and phosphatidylcholine and moderate amounts of aminolipids, phospholipid and sulfoquinovosyl diacylglycerol. Although ChimEc512(T) was able to nodulate A. vulneraria, the nodC and nifH genes were not detected by PCR. The rhizobial strain was tolerant to high concentrations of heavy metals: up to 35 mM Zn and up to 0.5 mM Cd and its growth kinetics was not impacted by Zn. The results of DNA-DNA hybridizations and physiological tests allowed genotypic and phenotypic differentiation of strain ChimEc512(T) from species of the genus Rhizobium with validly published names. Strain ChimEc512(T), therefore, represents a novel species, for which the name Rhizobium metallidurans sp. nov. is proposed, with the type strain

  12. Complete Genome Sequence of the Sesbania Symbiont and Rice Growth-Promoting Endophyte Rhizobium sp. Strain IRBG74

    PubMed Central

    Crook, Matthew B.; Mitra, Shubhajit; Ané, Jean-Michel

    2013-01-01

    Rhizobium sp. strain IRBG74 is the first known nitrogen-fixing symbiont in the Agrobacterium/Rhizobium clade that nodulates the aquatic legume Sesbania sp. and is also a growth-promoting endophyte of wetland rice. Here, we present the sequence of the IRBG74 genome, which is composed of a circular chromosome, a linear chromosome, and a symbiotic plasmid, pIRBG74a. PMID:24265489

  13. High quality draft genome sequence of Bacteroides barnesiae type strain BL2T (DSM 18169T) from chicken caecum

    SciTech Connect

    Sakamoto, Mitsuo; Lapidus, Alla L.; Han, James; Trong, Stephan; Haynes, Matthew; Reddy, T. B. K.; Mikhailova, Natalia; Huntemann, Marcel; Pati, Amrita; Ivanova, Natalia N.; Pukall, Rüdiger; Markowitz, Victor M.; Woyke, Tanja; Klenk, Hans-Peter; Kyrpides, Nikos C.; Ohkuma, Moriya

    2015-08-02

    Bacteroides barnesiae Lan et al. 2006 is a species of the genus Bacteroides, which belongs to the family Bacteroidaceae. Strain BL2T is of interest because it was isolated from the gut of a chicken and the growing awareness that the anaerobic microbiota of the caecum is of benefit for the host and may impact poultry farming. We report that the 3,621,509 bp long genome with its 3,059 protein-coding and 97 RNA genes is a part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project.

  14. Rhizobium meliloti mutants that overproduce the R. meliloti acidic Calcofluor-binding exopolysaccharide

    SciTech Connect

    Doherty, D.; Glazebrook, J.; Walker, G.C. ); Leigh, J.A. )

    1988-09-01

    The acidic Calcofluor-binding exopolysaccharide of Rhizobium meliloti Rm1021 plays one or more critical roles in nodule invasion and possible in nodule development. Two loci, exoR and exoS, that effect the regulation of synthesis of this exopolysaccharide were identified by screening for derivatives of strain Rm1021 that formed mucoid colonies that fluoresced extremely brightly under UV light when grown on medium containing Calcofluor. The exopolysaccharide produced in large quantities by the exoR95::Tn5 and exoS96::Tn5 strains was indistinguishable from that produced by the parental strain Rm1021, and its synthesis required the function of at least the exoA, exoB, and exoF genes. Both the exoR and exoS loci were located on the chromosome, and the exo96::Tn5 mutation was 84% linked to the trp-33 mutation by {Phi}M12 transduction. Synthesis of the Calcofluor-binding exopolysaccharide by strain Rm1021 was greatly stimulated by starvation for ammonia. In contrast, the exoR95::Tn5 mutant produced high levels of exopolysaccharide regardless of the presence or absence of ammonia in the medium. The exoS96::Tn5 mutant produced elevated amounts of exopolysaccharide in the presence of ammonia, but higher amounts were observed after starvation for ammonia. The presence of either mutation increased the level of expression of exoF::TnphoA and exoP::TnphoA fusions. Analyses of results obtained when alfalfa seedlings were inoculated with the exoR95::Tn5 strain indicated that the mutant strain could not invade nodules. However, pseudorevertants that retained the original exoR95::Tn5 mutant but acquired unlinked suppressors so that they produced an approximately normal amount of exopolysaccharide were able to invade nodules and fix nitrogen.

  15. Reactive Oxygen Species and Nitric Oxide Control Early Steps of the Legume - Rhizobium Symbiotic Interaction.

    PubMed

    Damiani, Isabelle; Pauly, Nicolas; Puppo, Alain; Brouquisse, Renaud; Boscari, Alexandre

    2016-01-01

    The symbiotic interaction between legumes and nitrogen-fixing rhizobium bacteria leads to the formation of a new organ, the nodule. Early steps of the interaction are characterized by the production of bacterial Nod factors, the reorientation of root-hair tip growth, the formation of an infection thread (IT) in the root hair, and the induction of cell division in inner cortical cells of the root, leading to a nodule primordium formation. Reactive oxygen species (ROS) and nitric oxide (NO) have been detected in early steps of the interaction. ROS/NO are determinant signals to arbitrate the specificity of this mutualistic association and modifications in their content impair the development of the symbiotic association. The decrease of ROS level prevents root hair curling and ITs formation, and that of NO conducts to delayed nodule formation. In root hairs, NADPH oxidases were shown to produce ROS which could be involved in the hair tip growth process. The use of enzyme inhibitors suggests that nitrate reductase and NO synthase-like enzymes are the main route for NO production during the early steps of the interaction. Transcriptomic analyses point to the involvement of ROS and NO in the success of the infection process, the induction of early nodulin gene expression, and the repression of plant defense, thereby favoring the establishment of the symbiosis. The occurrence of an interplay between ROS and NO was further supported by the finding of both S-sulfenylated and S-nitrosylated proteins during early symbiotic interaction, linking ROS/NO production to a redox-based regulation of the symbiotic process. PMID:27092165

  16. Reactive Oxygen Species and Nitric Oxide Control Early Steps of the Legume – Rhizobium Symbiotic Interaction

    PubMed Central

    Damiani, Isabelle; Pauly, Nicolas; Puppo, Alain; Brouquisse, Renaud; Boscari, Alexandre

    2016-01-01

    The symbiotic interaction between legumes and nitrogen-fixing rhizobium bacteria leads to the formation of a new organ, the nodule. Early steps of the interaction are characterized by the production of bacterial Nod factors, the reorientation of root-hair tip growth, the formation of an infection thread (IT) in the root hair, and the induction of cell division in inner cortical cells of the root, leading to a nodule primordium formation. Reactive oxygen species (ROS) and nitric oxide (NO) have been detected in early steps of the interaction. ROS/NO are determinant signals to arbitrate the specificity of this mutualistic association and modifications in their content impair the development of the symbiotic association. The decrease of ROS level prevents root hair curling and ITs formation, and that of NO conducts to delayed nodule formation. In root hairs, NADPH oxidases were shown to produce ROS which could be involved in the hair tip growth process. The use of enzyme inhibitors suggests that nitrate reductase and NO synthase-like enzymes are the main route for NO production during the early steps of the interaction. Transcriptomic analyses point to the involvement of ROS and NO in the success of the infection process, the induction of early nodulin gene expression, and the repression of plant defense, thereby favoring the establishment of the symbiosis. The occurrence of an interplay between ROS and NO was further supported by the finding of both S-sulfenylated and S-nitrosylated proteins during early symbiotic interaction, linking ROS/NO production to a redox-based regulation of the symbiotic process. PMID:27092165

  17. Activation of Bacteroides fragilis toxin by a novel bacterial protease contributes to anaerobic sepsis in mice.

    PubMed

    Choi, Vivian M; Herrou, Julien; Hecht, Aaron L; Teoh, Wei Ping; Turner, Jerrold R; Crosson, Sean; Bubeck Wardenburg, Juliane

    2016-05-01

    Bacteroides fragilis is the leading cause of anaerobic bacteremia and sepsis. Enterotoxigenic strains that produce B. fragilis toxin (BFT, fragilysin) contribute to colitis and intestinal malignancy, yet are also isolated in bloodstream infection. It is not known whether these strains harbor unique genetic determinants that confer virulence in extra-intestinal disease. We demonstrate that BFT contributes to sepsis in mice, and we identify a B. fragilis protease called fragipain (Fpn) that is required for the endogenous activation of BFT through the removal of its auto-inhibitory prodomain. Structural analysis of Fpn reveals a His-Cys catalytic dyad that is characteristic of C11-family cysteine proteases that are conserved in multiple pathogenic Bacteroides spp. and Clostridium spp. Fpn-deficient, enterotoxigenic B. fragilis has an attenuated ability to induce sepsis in mice; however, Fpn is dispensable in B. fragilis colitis, wherein host proteases mediate BFT activation. Our findings define a role for B. fragilis enterotoxin and its activating protease in the pathogenesis of bloodstream infection, which indicates a greater complexity of cellular targeting and activity of BFT than previously recognized. The expression of fpn by both toxigenic and nontoxigenic strains suggests that this protease may contribute to anaerobic sepsis in ways that extend beyond its role in toxin activation. It could thus potentially serve as a target for disease modification. PMID:27089515

  18. Heterogeneity in resistant fecal Bacteroides fragilis group collected from healthy people.

    PubMed

    Narimani, T; Douraghi, M; Owlia, P; Rastegar, A; Esghaei, M; Nasr, B; Talebi, M

    2016-06-01

    Normal nonpathogenic flora would represent a constant lake of resistance genes potentially transferable to human pathogens. To assess the prevalence of resistance genes and genetic variability of Bacteroides fragilis group (BFG) from normal flora, 177 Bacteroides isolates obtained from the fecal samples of healthy individuals. These isolates were subjected to antibiotic susceptibility testing and pulsed field gel electrophoresis (PFGE). The isolates were further tested for the presence of ermF, tetQ and bft genes by PCR. Our results indicated the presence of different clonal strains (1 common type and 57 single types) among the resistant isolates. The resistance rate for the six antibiotics in this study was between 1% and 95%. Most of the isolates (99%) were susceptible to metronidazole. ermF and tetQ were detected in all erythromycin and tetracycline resistant isolates. None of the isolates were carried bft gene. These data suggest dissemination of heterogenic clonal groups in healthy persons and resistance to 5 high commonly used antibiotics. PMID:26945562

  19. Identification and Phylogeny of the First T Cell Epitope Identified from a Human Gut Bacteroides Species

    PubMed Central

    Perez-Muñoz, Maria Elisa; Joglekar, Payal; Shen, Yi-Ji; Chang, Kuan Y.; Peterson, Daniel A.

    2015-01-01

    Host T cell reactivity toward gut bacterial epitopes has been recognized as part of disease pathogenesis. However, the specificity of T cells that recognize this vast number of epitopes has not yet been well described. After colonizing a C57BL/6J germ-free mouse with the human gut symbiotic bacteria Bacteroides thetaiotaomicron, we isolated a T cell that recognized these bacteria in vitro. Using this T cell, we mapped the first known non-carbohydrate T cell epitope within the phylum Bacteroidetes. The T cell also reacted to two other additional Bacteroides species. We identified the peptide that stimulated the T cell by using a genetic approach. Genomic data from the epitope-positive and epitope-negative bacteria explain the cross-reactivity of the T cell to multiple species. This epitope degeneracy should shape our understanding of the T cell repertoire stimulated by the complex microbiome residing in the gastrointestinal tract in both healthy and disease states. PMID:26637014

  20. Safety Assessment of Bacteroides uniformis CECT 7771 Isolated from Stools of Healthy Breast-Fed Infants

    PubMed Central

    Fernández-Murga, M. Leonor; Sanz, Yolanda

    2016-01-01

    Background Bacteroides uniformis CECT 7771 is a potential probiotic strain, originally isolated from the stools of healthy breast-feed infants. The strain showed pre-clinical efficacy in a mouse obesity model. The objective of this study was to evaluate its potential toxicity and translocation ability after acute oral administration to mice. Methods and Findings A safety study was conducted in immunocompetent and immunosuppressed C57BL-6 mice. Both mouse groups (n = 10 per group) were fed orally 2 x 109 colony forming units (cfu)/day of B. uniformis CECT 7771 or placebo by gavage for 6 days. Throughout this time, feed and water intake and body weight were monitored. Afterwards, mice were sacrificed and biological samples were collected to analyze blood and urine biochemistry, inflammatory and immune markers; gut mucosal histology and bacterial translocation to peripheral tissues. The results demonstrated that acute ingestion of this Bacteroides strain had no adverse effects on the animals’ general health status or food intake, nor did it affect biochemical indicators of liver, kidney and pancreatic function or gut mucosal histology. Findings also demonstrated that administration did not lead to bacterial translocation to blood, liver or mesenteric lymph nodes. B. uniformis CECT 7771 also downregulated gene and protein expression (iNOS and PPAR-γ) and inflammatory cytokines induced by immunosuppression. Conclusions The findings indicate that the acute oral consumption of B. uniformis CECT 7771 does not raise safety concerns in mice. Further studies in humans should be conducted. PMID:26784747

  1. Influence of heme and vitamin B12 on growth and fermentations of Bacteroides species.

    PubMed

    Chen, M; Wolin, M J

    1981-01-01

    We examined the effects of heme on the growth and fermentations of Bacteroides species. Bacteroides fragilis ATCC 25285 required heme for growth and produced malate and lactate as major products of glucose fermentation when the concentration of heme was 1 ng/ml. With 1 microgram of heme per ml, malate was not formed, lactate production decreased, and succinate and acetate were the major fermentation products. B. eggerthii ATCC 27754 grew without heme, with the production of mainly malate and lactate from glucose. Its fermentation with 1 microgram of heme per ml was similar to that of B. fragilis grown with the same concentration of heme. B. splanchicus VPI 6842 grew without heme, with the production of mainly malate, acetate, and H2 from glucose. With 1 microgram of heme per ml, malate disappeared, H2 decreased significantly, and succinate, acetate, and butyrate were the major products. The addition of vitamin B12 to media containing 1 microgram of heme per ml caused all species to produce propionate at the expense of succinate and, with B. splanchnicus, also at the expense of butyrate. Thus, the concentration of heme and the presence of vitamin B12 significantly influenced the course of glucose fermentation by these bacteria. PMID:7462148

  2. The methylome of the gut microbiome: disparate Dam methylation patterns in intestinal Bacteroides dorei

    PubMed Central

    Leonard, Michael T.; Davis-Richardson, Austin G.; Ardissone, Alexandria N.; Kemppainen, Kaisa M.; Drew, Jennifer C.; Ilonen, Jorma; Knip, Mikael; Simell, Olli; Toppari, Jorma; Veijola, Riitta; Hyöty, Heikki; Triplett, Eric W.

    2014-01-01

    Despite the large interest in the human microbiome in recent years, there are no reports of bacterial DNA methylation in the microbiome. Here metagenomic sequencing using the Pacific Biosciences platform allowed for rapid identification of bacterial GATC methylation status of a bacterial species in human stool samples. For this work, two stool samples were chosen that were dominated by a single species, Bacteroides dorei. Based on 16S rRNA analysis, this species represented over 45% of the bacteria present in these two samples. The B. dorei genome sequence from these samples was determined and the GATC methylation sites mapped. The Bacteroides dorei genome from one subject lacked any GATC methylation and lacked the DNA adenine methyltransferase genes. In contrast, B. dorei from another subject contained 20,551 methylated GATC sites. Of the 4970 open reading frames identified in the GATC methylated B. dorei genome, 3184 genes were methylated as well as 1735 GATC methylations in intergenic regions. These results suggest that DNA methylation patterns are important to consider in multi-omic analyses of microbiome samples seeking to discover the diversity of bacterial functions and may differ between disease states. PMID:25101067

  3. Characterization of the gene encoding nitrite reductase and the physiological consequences of its expression in the nondenitrifying Rhizobium {open_quotes}hedysari{close_quotes} strain HCNT1

    SciTech Connect

    Toffanin, A.; Shapleigh, J.P.; Maskus, M.

    1996-11-01

    Rhizobium {open_quotes}hedysari{close_quotes} HCNT1 is an unclassified rhizobium which contains a nitric oxide-producing nitrite reductase but is apparently incapable of coupling the reduction of nitrite to energy conservation. The gene encoding the nitrite reductase, nirK, has been cloned and sequenced and was found to encode a protein closely related to the copper-containing family of nitrite reductases. Unlike other members of this family, nirK expression in HCNT1 is not dependent on the presence of nitrogen oxides, being dependent only on oxygen concentration. Oxygen respiration of microaerobically grown Nir-deficient cells is not affected by concentrations of nitrite that completely inhibit oxygen respiration in wild-type cells. This loss of sensitivity suggests that the product of nitrite reductase, nitric oxide, is responsible for inhibition of oxygen respiration. By using a newly developed chemically modified electrode to detect nitric oxide, it was found that nitrite reduction by HCNT1 produces significantly higher nitric oxide concentrations than are observed in true denitrifiers. This indicates that nitrite reductase is the only nitrogen oxide reductase active in HCNT1. The capacity to generate such large concentrations of freely diffusible nitric oxide as a consequence of nitrite respiration makes HCNT1 unique among bacteria. 33 refs., 6 figs., 1 tab.

  4. Life in an Arsenic-Containing Gold Mine: Genome and Physiology of the Autotrophic Arsenite-Oxidizing Bacterium Rhizobium sp. NT-26

    PubMed Central

    Andres, Jérémy; Arsène-Ploetze, Florence; Barbe, Valérie; Brochier-Armanet, Céline; Cleiss-Arnold, Jessica; Coppée, Jean-Yves; Dillies, Marie-Agnès; Geist, Lucie; Joublin, Aurélie; Koechler, Sandrine; Lassalle, Florent; Marchal, Marie; Médigue, Claudine; Muller, Daniel; Nesme, Xavier; Plewniak, Frédéric; Proux, Caroline; Ramírez-Bahena, Martha Helena; Schenowitz, Chantal; Sismeiro, Odile; Vallenet, David; Santini, Joanne M.; Bertin, Philippe N.

    2013-01-01

    Arsenic is widespread in the environment and its presence is a result of natural or anthropogenic activities. Microbes have developed different mechanisms to deal with toxic compounds such as arsenic and this is to resist or metabolize the compound. Here, we present the first reference set of genomic, transcriptomic and proteomic data of an Alphaproteobacterium isolated from an arsenic-containing goldmine: Rhizobium sp. NT-26. Although phylogenetically related to the plant-associated bacteria, this organism has lost the major colonizing capabilities needed for symbiosis with legumes. In contrast, the genome of Rhizobium sp. NT-26 comprises a megaplasmid containing the various genes, which enable it to metabolize arsenite. Remarkably, although the genes required for arsenite oxidation and flagellar motility/biofilm formation are carried by the megaplasmid and the chromosome, respectively, a coordinate regulation of these two mechanisms was observed. Taken together, these processes illustrate the impact environmental pressure can have on the evolution of bacterial genomes, improving the fitness of bacterial strains by the acquisition of novel functions. PMID:23589360

  5. Terminal Bacteroid Differentiation Is Associated With Variable Morphological Changes in Legume Species Belonging to the Inverted Repeat-Lacking Clade.

    PubMed

    Montiel, Jesús; Szűcs, Attila; Boboescu, Iulian Z; Gherman, Vasile D; Kondorosi, Éva; Kereszt, Attila

    2016-03-01

    Medicago and closely related legume species from the inverted repeat-lacking clade (IRLC) impose terminal differentiation onto their bacterial endosymbionts, manifested in genome endoreduplication, cell enlargement, and loss of cell-division capacity. Nodule-specific cysteine-rich (NCR) secreted host peptides are plant effectors of this process. As bacteroids in other IRLC legumes, such as Cicer arietinum and Glycyrrhiza lepidota, were reported not to display features of terminal differentiation, we investigated the fate of bacteroids in species from these genera as well as in four other species representing distinct genera of the phylogenetic tree for this clade. Bacteroids in all tested legumes proved to be larger in size and DNA content than cultured cells; however, the degree of cell elongation was rather variable in the different species. In addition, the reproductive ability of the bacteroids isolated from these legumes was remarkably reduced. In all IRLC species with available sequence data, the existence of NCR genes was found. These results indicate that IRLC legumes provoke terminal differentiation of their endosymbionts with different morphotypes, probably with the help of NCR peptides. PMID:26713350

  6. Comparison of Bacteroides-Prevotella 16S rRNA genetic markers for fecal samples from different animal species

    USGS Publications Warehouse

    Fogarty, L.R.; Voytek, M.A.

    2005-01-01

    To effectively manage surface and ground waters it is necessary to improve our ability to detect and identify sources of fecal contamination. We evaluated the use of the anaerobic bacterial group Bacteroides-Prevotella as a potential fecal indicator. Terminal restriction length polymorphism (T-RFLP) of the 16S rRNA genes from this group was used to determine differences in populations and to identify any unique populations in chickens, cows, deer, dogs, geese, horses, humans, pigs, and seagulls. The group appears to be a good potential fecal indicator in all groups tested except for avians. Cluster analysis of Bacteroides-Prevotella community T-RFLP profiles indicates that Bacteroides-Prevotella populations from samples of the same host species are much more similar to each other than to samples from different source species. We were unable to identify unique peaks that were exclusive to any source species; however, for most host species, at least one T-RFLP peak was identified to be more commonly found in that species, and a combination of peaks could be used to identify the source. T-RFLP profiles obtained from water spiked with known-source feces contained the expected diagnostic peaks from the source. These results indicate that the approach of identifying Bacteroides-Prevotella molecular markers associated with host species might be useful in identifying sources of fecal contamination in the environment.

  7. A new chromogenic medium for isolation of Bacteroides fragilis suitable for screening for strains with antimicrobial resistance.

    PubMed

    Tierney, Daniel; Copsey, Sarah D; Morris, Trefor; Perry, John D

    2016-06-01

    There have been an increasing number of reports describing the acquisition of antimicrobial resistance by Bacteroides fragilis including the occurrence of strains with resistance to multiple antimicrobials that are relied upon for treatment of infections. The aim of this study was to design a chromogenic selective medium for isolation of B. fragilis that could be adapted for specific isolation of antimicrobial-resistant strains. Bacteroides chromogenic agar (BCA) was the result of this endeavour and allowed growth of Bacteroides spp. as black colonies and the efficient inhibition of almost all other genera tested. The medium also allowed some differentiation of B. fragilis from other members of the B. fragilis group. When compared with an adaptation of Bacteroides bile-esculin agar (BBE) for the isolation of B. fragilis from 100 stool samples, 30 isolates of B. fragilis were recovered on BCA compared with 19 isolates recovered on BBE (P = 0.022). When supplemented with meropenem (4 μg/ml) or metronidazole (2 μg/ml), BCA could be used to select for the growth of B. fragilis isolates with resistance to these agents. We conclude that BCA is a useful research tool for surveillance studies to assess the prevalence of B. fragilis and, in particular, the occurrence of antimicrobial-resistant strains. PMID:27060277

  8. Evaluation of Bacteroides fragilis GB-124 bacteriophages as novel human-associated faecal indicators in the United States

    EPA Science Inventory

    Phages infecting human-associated Bacteroides fragilis (GB-124 phages) have been employed in the European Union (EU) to identify human fecal pollution, but their utility for U.S. was unclear. Primary sewage effluent samples were collected seasonally from seven wastewater treatme...

  9. Improved HF183 reverse primer and probe for greater analytical sensitivity of human bacteroides in the environment

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: Numerous indicators have been used to assess the presence of fecal pollution, many relying on molecular methods such as qPCR. One of the targets frequently used, the human-specific Bacteroides 16s rRNA genetic marker, has several assays in current usage. These assays vary in terms of t...

  10. Comparison of bacteroides-prevotella 16S rRNA genetic markers for fecal samples from different animal species.

    PubMed

    Fogarty, Lisa R; Voytek, Mary A

    2005-10-01

    To effectively manage surface and ground waters it is necessary to improve our ability to detect and identify sources of fecal contamination. We evaluated the use of the anaerobic bacterial group Bacteroides-Prevotella as a potential fecal indicator. Terminal restriction length polymorphism (T-RFLP) of the 16S rRNA genes from this group was used to determine differences in populations and to identify any unique populations in chickens, cows, deer, dogs, geese, horses, humans, pigs, and seagulls. The group appears to be a good potential fecal indicator in all groups tested except for avians. Cluster analysis of Bacteroides-Prevotella community T-RFLP profiles indicates that Bacteroides-Prevotella populations from samples of the same host species are much more similar to each other than to samples from different source species. We were unable to identify unique peaks that were exclusive to any source species; however, for most host species, at least one T-RFLP peak was identified to be more commonly found in that species, and a combination of peaks could be used to identify the source. T-RFLP profiles obtained from water spiked with known-source feces contained the expected diagnostic peaks from the source. These results indicate that the approach of identifying Bacteroides-Prevotella molecular markers associated with host species might be useful in identifying sources of fecal contamination in the environment. PMID:16204514

  11. Regulated expression of polysaccharide utilization and capsular biosynthesis loci in biofilm and planktonic Bacteroides thetaiotaomicron during growth in chemostats

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bacteroides thetaiotaomicron is a prominent member of the human distal gut microbiota that specializes in breaking down diet and host-derived polysaccharides. While polysaccharide utilization has been well studied in B. thetaiotaomicron, other aspects of its behavior are less well characterized, in...

  12. Improved HF183 reverse primer and probe for greater analytical sensitivity of human Bacteroides in the environment

    EPA Science Inventory

    Background: Numerous indicators have been used to assess the presence of fecal pollution, many relying on molecular methods such as qPCR. One of the targets frequently used, the human-associated Bacteroides 16s rRNA region, has several assays in current usage. These assays vary...

  13. Identification and Use of the Putative Bacteroides ovatus Xylanase Promoter for the Inducible Production of Recombinant Human Proteins

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The use of genetically modified bacteria to deliver biologically active molecules directly to the gut has become an increasingly attractive area of investigation. The challenge of regulation of production of the therapeutic molecule and colonization of the bowel led us to investigate Bacteroides ov...

  14. Bacteroides fragilis in biopsies of patients with major abscesses and diabetic foot infections: direct molecular versus culture-based detection.

    PubMed

    Stappers, Mark H T; Hagen, Ferry; Reimnitz, Peter; Mouton, Johan W; Meis, Jacques F; Gyssens, Inge C

    2016-06-01

    Direct determination by pathogen-specific real-time PCR assay for Bacteroides fragilis was compared to culture in major abscess and diabetic foot infection biopsy samples. Real-time PCR resulted in an increased detection rate of 12% for B. fragilis and could improve the detection of B. fragilis in clinical samples. PMID:27112830

  15. Phylogenetic relationships and host range of Rhizobium spp. that nodulate Phaseolus vulgaris L.

    PubMed Central

    Hernandez-Lucas, I; Segovia, L; Martinez-Romero, E; Pueppke, S G

    1995-01-01

    We determined the nucleotide sequences of 16S rRNA gene segments from five Rhizobium strains that have been isolated from tropical legume species. All share the capacity to nodulate Phaseolus vulgaris L., the common bean. Phylogenetic analysis confirmed that these strains are of two different chromosomal lineages. We defined the host ranges of two strains of Rhizobium etli and three strains of R. tropici, comparing them with those of the two most divergently related new strains. Twenty-two of the 43 tested legume species were nodulated by three or more of these strains. All seven strains have broad host ranges that include woody species such as Albizia lebbeck, Gliricidia maculata, and Leucaena leucocephala. PMID:7618891

  16. Transfer of R factors to and between genetically marked sublines of Rhizobium japonicum.

    PubMed

    Kuykendall, L D

    1979-05-01

    Plasmids R1822 and pRD1 of the P-1 incompatibility group, for which Rhizobium japonicum had not previously been shown to serve as host, were introduced into a strain of R. japonicum. Acquisition of R68 and R68.45 plasmids by this Rhizobium was equivocal. Transfer of R1822 from Pseudomonas aeruginosa and of pRD1 from Escherichia coli to R. japonicum was unambiguous, because the exconjugants subsequently cotransferred the three R-factor resistance determinants (kanamycin, tetracycline, and penicillin) between genetically marked sublines of strain I-110. Under optimal conditions the transfer of R1822 and pRD1 occurred at frequencies of approximately 10(-3) in plate matings of strains bearing as many as five dissimilar genetic markers. In matings with R1822 on membrane filters, recombinants were formed at incidences as high as 4%. PMID:114109

  17. Narrow- and Broad-Host-Range Symbiotic Plasmids of Rhizobium spp. Strains That Nodulate Phaseolus vulgaris

    PubMed Central

    Brom, Susana; Martinez, Esperanza; Dávila, Guillermo; Palacios, Rafael

    1988-01-01

    Agrobacterium transconjugants containing symbiotic plasmids from different Rhizobium spp. strains that nodulate Phaseolus vulgaris were obtained. All transconjugants conserved the parental nodulation host range. Symbiotic (Sym) plasmids of Rhizobium strains isolated originally from P. vulgaris nodules, which had a broad nodulation host range, and single-copy nitrogenase genes conferred a Fix+ phenotype to the Agrobacterium transconjugants. A Fix− phenotype was obtained with Sym plasmids of strains isolated from P. vulgaris nodules that had a narrow host range and reiterated nif genes, as well as with Sym plasmids of strains isolated from other legumes that presented single nif genes and a broad nodulation host range. This indicates that different types of Sym plasmids can confer the ability to establish an effective symbiosis with P. vulgaris. Images PMID:16347637

  18. Three Replicons of Rhizobium sp. Strain NGR234 Harbor Symbiotic Gene Sequences

    PubMed Central

    Flores, Margarita; Mavingui, Patrick; Girard, Lourdes; Perret, Xavier; Broughton, William J.; Martínez-Romero, Esperanza; Dávila, Guillermo; Palacios, Rafael

    1998-01-01

    Rhizobium sp. strain NGR234 contains three replicons: the symbiotic plasmid or pNGR234a, a megaplasmid (pNGR234b), and the chromosome. Symbiotic gene sequences not present in pNGR234a were analyzed by hybridization. DNA sequences homologous to the genes fixLJKNOPQGHIS were found on the chromosome, while sequences homologous to nodPQ and exoBDFLK were found on pNGR234b. PMID:9811668

  19. Rhizobium anhuiense as the predominant microsymbionts of Lathyrus maritimus along the Shandong Peninsula seashore line.

    PubMed

    Li, Yan; Wang, En Tao; Liu, Yajing; Li, Xiangyue; Yu, Bing; Ren, Chenggang; Liu, Wei; Li, Yunzhao; Xie, Zhihong

    2016-09-01

    Beach pea [Lathyrus maritimus Bigelow, or Lathyrus japonicus subsp. maritimus (L.) P.W. Ball] is a wild legume distributed on the seashore line, and the rhizobia nodulating with this plant have been reported only rarely. In order to reveal the diversity of beach pea rhizobia on the seashore line of Shandong Peninsula, China, a total of 124 bacterial strains were isolated from the root nodules of beach pea plants collected from five sites. All the isolates were divided into five recA types after screening by recA gene sequence analysis and they consisted of Rhizobium anhuiense covering 122 symbiotic isolates in three recA types, as well as two single isolates Rhizobium sp. and Rhizobium lusitanum representing distinct recA types. The recA genotype III of R. anhuiense (103 isolates) represented by strain YIC11270 was dominant at all five sampling sites. Identical symbiotic genes (nodC and nifH) were detected in the three recA genotypes of R. anhuiense isolates that were closely related to those of the pea and faba rhizobia. This study clarified that R. anhuiense was the main symbiont for beach pea rhizobia on the seashore line of Shandong Peninsula. The low level genetic diversity of beach pea rhizobia revealed by both MLSA and the symbiotic genes might be related to the strong selection pressure produced by the saline-alkaline environment and the host plants. PMID:27480059

  20. Isolation of monoclonal antibodies reacting with the core component of lipopolysaccharide from Rhizobium leguminosarum strain 3841 and mutant derivatives.

    PubMed Central

    Lucas, M M; Peart, J L; Brewin, N J; Kannenberg, E L

    1996-01-01

    Monoclonal antibodies reacting with the core oligosaccharide or lipid A component of Rhizobium lipopolysaccharide (LPS) could be useful for the elucidation of the structure and biosynthesis of this group of macromolecules. Mutant derivatives of Rhizobium leguminosarum 3841 with LPS structures lacking the major O-antigen moiety were used as immunogens, and eight antibodies were selected for further study. All the antibodies reacted with the fast-migrating species known as LPS-2 following gel electrophoresis of Rhizobium cell extracts. For four of these antibodies, reactivity with affinity-purified LPS was lost after mild acid hydrolysis, indicating that they probably recognized the core oligosaccharide component. The four other antibodies still reacted with acid-treated LPS and may recognize the lipid A moiety, which is stable to mild acid hydrolysis. The pattern of antibody staining after gel electrophoresis revealed differences in LPS-2 epitope structure between each of the mutants and the wild type. Furthermore, for each of the mutants the antibodies crossreacted with a minor band that migrated more slowly than LPS-2; we have termed this more slowly migrating form LPS-3. The majority of the antibodies also reacted with LPS from strain CE109, a derivative of Rhizobium etli CE3, confirming that the LPS core antigens can be relatively conserved between strains of different Rhizobium species. One of the antibodies isolated in this study (JIM 32) was unusual because it appeared to react with all forms of LPS from strain 3841 (namely, LPS-1, LPS-2, and LPS-3). Furthermore, JIM 32 reacted positively with the LPS from many strains of Rhizobium tested (excluding the Rhizobium meliloti subgroup). JIM 32 did not react with representative strains from Bradyrhizobium, Azorhizobium or other related bacterial species. PMID:8631658

  1. Rhizobium flavum sp. nov., a triazophos-degrading bacterium isolated from soil under the long-term application of triazophos.

    PubMed

    Gu, Tao; Sun, Li Na; Zhang, Jun; Sui, Xin Hua; Li, Shun Peng

    2014-06-01

    A Gram-stain-negative, non-motile, pale yellow, rod-shaped bacterial strain, YW14(T), was isolated from soil and its taxonomic position was investigated by a polyphasic study. Strain YW14(T) did not form nodules on three different legumes, and the nodD and nifH genes were not detected by PCR. Strain YW14(T) contained Q-10 as the predominant ubiquinone. The major cellular fatty acid was C(18 : 1)ω7c. Phylogenetic analyses based on 16S rRNA gene sequences and seven housekeeping gene sequences (recA, atpD, glnII, gyrB, rpoB, dnaK and thrC) showed that strain YW14(T) belonged to the genus Rhizobium. Strain YW14(T) showed 16S rRNA gene sequence similarity of 93.4-97.3% to the type strains of recognized species of the genus Rhizobium. DNA-DNA relatedness between strain YW14(T) and the type strains of Rhizobium sullae IS123(T) and Rhizobium yanglingense CCBAU 71623(T) was 19.6-25.7%, indicating that strain YW14(T) was distinct from them genetically. Strain YW14(T) could also be differentiated from these phylogenetically related species of the genus Rhizobium by various phenotypic properties. On the basis of phenotypic properties, phylogenetic distinctiveness and genetic data, strain YW14(T) is considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium flavum sp. nov. is proposed. The type strain is YW14(T) ( = KACC 17222(T) = CCTCC AB2013042(T)). PMID:24639241

  2. Multiple Mobile Promoter Regions for the Rare Carbapenem Resistance Gene of Bacteroides fragilis

    PubMed Central

    Podglajen, I.; Breuil, J.; Rohaut, A.; Monsempes, C.; Collatz, E.

    2001-01-01

    Two novel insertion sequences (IS), IS1187 and IS1188, are described upstream from the carbapenem resistance gene cfiA in strains of Bacteroides fragilis. Mapping, with the RACE procedure, of transcription start sites of cfiA in these and two other previously reported IS showed that transcription of this rarely encountered gene is initiated close to a variety of B. fragilis consensus promoter sequences, as recently defined (D. P. Bayley, E. R. Rocha, and C. J. Smith, FEMS Microbiol. Lett. 193:149–154, 2000). In the cases of IS1186 and IS1188, these sequences overlap with putative Eς70 promoter sequences, while in IS942 and IS1187 such sequences can be observed either upstream or downstream of the B. fragilis promoters. PMID:11344163

  3. Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides.

    PubMed

    Wu, Meng; McNulty, Nathan P; Rodionov, Dmitry A; Khoroshkin, Matvei S; Griffin, Nicholas W; Cheng, Jiye; Latreille, Phil; Kerstetter, Randall A; Terrapon, Nicolas; Henrissat, Bernard; Osterman, Andrei L; Gordon, Jeffrey I

    2015-10-01

    Libraries of tens of thousands of transposon mutants generated from each of four human gut Bacteroides strains, two representing the same species, were introduced simultaneously into gnotobiotic mice together with 11 other wild-type strains to generate a 15-member artificial human gut microbiota. Mice received one of two distinct diets monotonously, or both in different ordered sequences. Quantifying the abundance of mutants in different diet contexts allowed gene-level characterization of fitness determinants, niche, stability, and resilience and yielded a prebiotic (arabinoxylan) that allowed targeted manipulation of the community. The approach described is generalizable and should be useful for defining mechanisms critical for sustaining and/or approaches for deliberately reconfiguring the highly adaptive and durable relationship between the human gut microbiota and host in ways that promote wellness. PMID:26430127

  4. Bacteroides fragilis induce necrosis on mice peritoneal macrophages: In vitro and in vivo assays

    SciTech Connect

    Vieira, J.M.B.D.; Seabra, S.H.; Vallim, D.C.; Americo, M.A.; Fracallanza, S.E.L.; Vommaro, R.C.; Domingues, R.M.C.P.

    2009-10-02

    Bacteroides fragilis is an anaerobic bacteria component of human intestinal microbiota and agent of infections. In the host B. fragilis interacts with macrophages, which produces toxic radicals like NO. The interaction of activated mice peritoneal macrophages with four strains of B. fragilis was evaluated on this study. Previously was shown that such strains could cause metabolic and morphologic alterations related to macrophage death. In this work propidium iodide staining showed the strains inducing macrophage necrosis in that the labeling was evident. Besides nitroblue tetrazolium test showed that B. fragilis stimulates macrophage to produce oxygen radicals. In vivo assays performed in BalbC mice have results similar to those for in vitro tests as well as scanning electron microscopy, which showed the same surface pore-like structures observed in vitro before. The results revealed that B. fragilis strains studied lead to macrophage death by a process similar to necrosis.

  5. Symbiotic Relationship of Bacteroides cellulosolvens and Clostridium saccharolyticum in Cellulose Fermentation†

    PubMed Central

    Murray, William D.

    1986-01-01

    In coculture, Bacteroides cellulosolvens and Clostridium saccharolyticum fermented 33% more cellulose than did B. cellulosolvens alone. Also, cellulose digestion continued at a maximum rate 48 h longer in coculture. B. cellulosolvens hydrolyzes cellulose and supplies C. saccharolyticum with sugars and a growth factor replaceable by yeast extract. Alone, B. cellulosolvens exhibited an early cessation of growth which was not due to nutrient depletion, low pH, or toxic accumulation of acetic acid, ethanol, lactic acid, H2, CO2, cellobiose, glucose, or xylose. However, a 1-h incubation of B. cellulosolvens spent-culture medium with C. saacharolyticum cells starved for growth factor allowed a resumption of B. cellulosolvens growth. The symbiotic relationship of this naturally occurring coculture is one of mutualism, in which the cellulolytic microbe supplies the saccharolytic microbe with nutrients, and in turn the saccharolytic microbe removes a secondary metabolite toxic to the primary microbe. Images PMID:16347034

  6. Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides

    PubMed Central

    Wu, Meng; McNulty, Nathan P.; Rodionov, Dmitry A.; Khoroshkin, Matvei S.; Griffin, Nicholas W.; Cheng, Jiye; Latreille, Phil; Kerstetter, Randall A.; Terrapon, Nicolas; Henrissat, Bernard; Osterman, Andrei L.; Gordon, Jeffrey I.

    2015-01-01

    Libraries of tens of thousands of transposon mutants generated from each of four human gut Bacteroides strains, two representing the same species, were introduced simultaneously into gnotobiotic mice together with 11 other wild-type strains to generate a 15-member artificial human gut microbiota. Mice received one of two distinct diets monotonously, or both in ordered sequence. Quantifying the abundance of mutants in different diet contexts allowed gene-level characterization of fitness determinants, niche, stability and resilience, and yielded a prebiotic (arabinoxylan) that allowed targeted manipulation of the community. The approach described is generalizable and should be useful for defining mechanisms critical for sustaining and/or approaches for deliberately reconfiguring the highly adaptive and durable relationship between the human gut microbiota and host in ways that promote wellness. PMID:26430127

  7. UDP-Glucuronic Acid Decarboxylases of Bacteroides fragilis and Their Prevalence in Bacteria▿†

    PubMed Central

    Coyne, Michael J.; Fletcher, C. Mark; Reinap, Barbara; Comstock, Laurie E.

    2011-01-01

    Xylose is rarely described as a component of bacterial glycans. UDP-xylose is the nucleotide-activated form necessary for incorporation of xylose into glycans and is synthesized by the decarboxylation of UDP-glucuronic acid (UDP-GlcA). Enzymes with UDP-GlcA decarboxylase activity include those that lead to the formation of UDP-xylose as the end product (Uxs type) and those synthesizing UDP-xylose as an intermediate (ArnA and RsU4kpxs types). In this report, we identify and confirm the activities of two Uxs-type UDP-GlcA decarboxylases of Bacteroides fragilis, designated BfUxs1 and BfUxs2. Bfuxs1 is located in a conserved region of the B. fragilis genome, whereas Bfuxs2 is in the heterogeneous capsular polysaccharide F (PSF) biosynthesis locus. Deletion of either gene separately does not result in the loss of a detectable phenotype, but deletion of both genes abrogates PSF synthesis, strongly suggesting that they are functional paralogs and that the B. fragilis NCTC 9343 PSF repeat unit contains xylose. UDP-GlcA decarboxylases are often annotated incorrectly as NAD-dependent epimerases/dehydratases; therefore, their prevalence in bacteria is underappreciated. Using available structural and mutational data, we devised a sequence pattern to detect bacterial genes encoding UDP-GlcA decarboxylase activity. We identified 826 predicted UDP-GlcA decarboxylase enzymes in diverse bacterial species, with the ArnA and RsU4kpxs types confined largely to proteobacterial species. These data suggest that xylose, or a monosaccharide requiring a UDP-xylose intermediate, is more prevalent in bacterial glycans than previously appreciated. Genes encoding BfUxs1-like enzymes are highly conserved in Bacteroides species, indicating that these abundant intestinal microbes may synthesize a conserved xylose-containing glycan. PMID:21804000

  8. Bacteroides gingivalis-Actinomyces viscosus cohesive interactions as measured by a quantitative binding assay

    SciTech Connect

    Schwarz, S.; Ellen, R.P.; Grove, D.A.

    1987-10-01

    There is limited evidence, mostly indirect, to suggest that the adherence of Bacteroides gingivalis to teeth may be enhanced by the presence of gram-positive dental plaque bacteria like Actinomyces viscosus. The purpose of this study was to carry out direct quantitative assessments of the cohesion of B gingivalis and A. viscosus by using an in vitro assay modeled on the natural sequence in which these two species colonize the teeth. The assay allowed comparisons to be made of the adherence of /sup 3/H-labeled B. gingivalis 2561 and 381 to saliva-coated hydroxyapatite beads (S-HA) and A. viscosus WVU627- or T14V-coated S-HA (actinobeads) in equilibrium and kinetics binding studies. A series of preliminary binding studies with 3H-labeled A. viscosus and parallel studies by scanning electron microscopy with unlabeled A. viscosus were conducted to establish a protocol by which actinobeads suitable for subsequent Bacteroides adherence experiments could be prepared. By scanning electron microscopy, the actinobeads had only small gaps of exposed S-HA between essentially irreversibly bound A. viscosus cells. Furthermore, B. gingivalis cells appeared to bind preferentially to the Actinomyces cells instead of the exposed S-HA. B. gingivalis binding to both S-HA and actinobeads was saturable with at least 2 X 10(9) to 3 X 10(9) cells per ml, and equilibrium with saturating concentrations was reached within 10 to 20 min. B. gingivalis always bound in greater numbers to the actinobeads than to S-HA. These findings provide direct measurements supporting the concept that cohesion with dental plaque bacteria like A. viscosus may foster the establishment of B. gingivalis on teeth by enhancing its adherence.

  9. Rhizobium straminoryzae sp. nov., isolated from the surface of rice straw.

    PubMed

    Lin, Shih-Yao; Hsu, Yi-Han; Liu, You-Cheng; Hung, Mei-Hua; Hameed, Asif; Lai, Wei-An; Yen, Wen-Shao; Young, Chiu-Chung

    2014-09-01

    An aerobic, Gram-stain-negative, rod-shaped bacterium, designated strain CC-LY845(T), was isolated from the surface of rice straw in Taiwan. Cells were non-motile, and no flagellum was detected. Comparison of 16S rRNA gene sequences indicated that the strain was phylogenetically related to species of the genus Rhizobium, with closest similarity to Rhizobium pseudoryzae KCTC 23294(T) (97.6 %), R. rhizoryzae KCTC 23652(T) (97.0 %) and R. oryzae LMG 24253(T) (96.7 %); other species showed lower levels of similarity (<96.6 %). The DNA-DNA relatedness of strain CC-LY845(T) and R. pseudoryzae KCTC 23294(T) was 34.8±3.1 % (reciprocal value 39.2±2.2 %). Phylogenetic analysis based on the housekeeping atpD and recA genes showed that the novel strain could be distinguished from R. pseudoryzae KCTC 23294(T) (92.7 and 91.5 %, respectively) and other species of the genus Rhizobium. The temperature range for growth was 25-42 °C, the pH range was 5.0-9.0 and NaCl concentrations up to 4.0 % (w/v) were tolerated. Strain CC-LY845(T) did not form nodules on four different legumes, and the nodD and nifH genes were not detected by PCR. The major fatty acids were C16 : 0 and summed feature 8 (C18 : 1ω7c/C18 : 1ω6c). The polyamine pattern of strain CC-LY845(T) showed spermidine and putrescine as major polyamines. The predominant quinone system was ubiquinone 10 (Q-10). The DNA G+C content was 68.3±2.4 mol%. Base on its phylogenetic, phenotypic and chemotaxonomic features, strain CC-LY845(T) is proposed to represent a novel species within the genus Rhizobium, for which the name Rhizobium straminoryzae sp. nov. is proposed. The type strain is strain CC-LY845(T) ( = BCRC 80698(T) = JCM 19536(T)). PMID:24899657

  10. Rhizobium capsici sp. nov., isolated from root tumor of a green bell pepper (Capsicum annuum var. grossum) plant.

    PubMed

    Lin, Shih-Yao; Hung, Mei-Hua; Hameed, Asif; Liu, You-Cheng; Hsu, Yi-Han; Wen, Cheng-Zhe; Arun, A B; Busse, Hans-Jürgen; Glaeser, Stefanie P; Kämpfer, Peter; Young, Chiu-Chung

    2015-03-01

    A novel, Gram-staining-negative, rod-shaped, aerobic and motile bacterium, designated strain CC-SKC2(T), was isolated from the root tumor of a green bell pepper (Capsicum annuum var. grossum) plant in Taiwan. Cells were positive for oxidase and catalase activities and exhibited growth at 25-37 °C, pH 4.0-9.0 and tolerated NaCl concentrations up to 4.0 % (w/v). Strain CC-SKC2(T) is able to trigger nodulation in soybean (Glycine max Merr.), but not in Capsicum annuum var. grossum, red bean (Vigna angularis), sesbania (Sesbania roxburghii Merr.) or alfalfa (Medicago varia Martin.). The novel strain shared highest 16S rRNA gene sequence similarity to Rhizobium rhizoryzae KCTC 23652(T) and Rhizobium straminoryzae CC-LY845(T) (both 97.5 %) followed by Rhizobium lemnae L6-16(T) (97.3 %), Rhizobium pseudoryzae KCTC 23294(T) (97.1 %), and Rhizobium paknamense NBRC 109338(T) (97.0 %), whereas other Rhizobium species shared <96.7 % similarity. The DNA-DNA relatedness values of strain CC-SKC2(T) with R. rhizoryzae KCTC 23652(T), R. pseudoryzae KCTC 23294(T) and R. paknamense NBRC 109338(T) were 11.4, 17.2 and 17.0 %, respectively (reciprocal values were 11.1, 28.3 and 24.0 %, respectively). Phylogenetic analysis based on 16S rRNA, atpD and recA genes revealed a distinct taxonomic position attained by strain CC-SKC2(T) with respect to other Rhizobium species. The major fatty acids in strain CC-SKC2(T) were C16:0, C19:0 cyclo ω8c, C14:0 3-OH and/or C16:1 iso I and C18:1 ω7c and/or C18:1 ω6c. The polyamine pattern showed predominance of spermidine and moderate amounts of sym-homospermidine. The predominant quinone system was ubiquinone (Q-10) and the DNA G+C content was 60.5 mol%. On the basis of polyphasic taxonomic evidence presented here, strain CC-SKC2(T) is proposed to represent a novel species within the genus Rhizobium, for which the name Rhizobium capsici sp. nov. is proposed. The type strain is CC-SKC2(T) (=BCRC 80699(T) = JCM 19535(T)). PMID:25555455

  11. Quantitative PCR assay of sewage-associated Bacteroides markers to assess sewage pollution in an urban lake in Dhaka, Bangladesh.

    PubMed

    Ahmed, Warish; Yusuf, Rita; Hasan, Imtiaj; Goonetilleke, Ashantha; Gardner, Ted

    2010-10-01

    This paper aimed to assess the magnitude of sewage pollution in an urban lake in Dhaka, Bangladesh, by using quantitative PCR of sewage-associated Bacteroides HF183 markers. PCR was also used for the quantitative detection of ruminant wastewater-associated CF128 markers along with the enumeration of traditional fecal indicator bacteria, namely enterococci. The number of enterococci in lake water samples ranged from 1.1 × 10⁴ to 1.9 × 10⁵ colony-forming units/100 mL water. From the 20 water samples tested, 14 (70%) and 7 (35%) were PCR positive for HF183 and CF128 markers, respectively. The numbers of HF183 and CF128 markers in lake water samples were 3.9 × 10⁴ to 6.3 × 10⁷ and 9.3 × 10³ to 6.3 × 10⁵ genomic units/100 mL water, respectively. The high numbers of enterococci and HF183 markers are indicative of sewage pollution and potential health risks to those who use the lake water for nonpotable purposes such as bathing and washing clothes. This is the first study that investigated the presence of microbial source tracking markers in Dhaka, Bangladesh, where diarrhoeal disease is one of the major causes of childhood mortality. The molecular assay used in this study can provide valuable information on the extent of sewage pollution, thus facilitating the development of robust strategies to minimize potential health risks. PMID:20962907

  12. Sugar-binding activity of pea lectin enhances heterologous infection of transgenic alfalfa plants by Rhizobium leguminosarum biovar viciae.

    PubMed

    van Rhijn, P; Fujishige, N A; Lim, P O; Hirsch, A M

    2001-05-01

    Transgenic alfalfa (Medicago sativa L. cv Regen) roots carrying genes encoding soybean lectin or pea (Pisum sativum) seed lectin (PSL) were inoculated with Bradyrhizobium japonicum or Rhizobium leguminosarum bv viciae, respectively, and their responses were compared with those of comparably inoculated control plants. We found that nodule-like structures formed on alfalfa roots only when the rhizobial strains produced Nod factor from the alfalfa-nodulating strain, Sinorhizobium meliloti. Uninfected nodule-like structures developed on the soybean lectin-transgenic plant roots at very low inoculum concentrations, but bona fide infection threads were not detected even when B. japonicum produced the appropriate S. meliloti Nod factor. In contrast, the PSL-transgenic plants were not only well nodulated but also exhibited infection thread formation in response to R. leguminosarum bv viciae, but only when the bacteria expressed the complete set of S. meliloti nod genes. A few nodules from the PSL-transgenic plant roots were even found to be colonized by R. leguminosarum bv viciae expressing S. meliloti nod genes, but the plants were yellow and senescent, indicating that nitrogen fixation did not take place. Exopolysaccharide appears to be absolutely required for both nodule development and infection thread formation because neither occurred in PSL-transgenic plant roots following inoculation with an Exo(-) R. leguminosarum bv viciae strain that produced S. meliloti Nod factor. PMID:11351077

  13. Sugar-Binding Activity of Pea Lectin Enhances Heterologous Infection of Transgenic Alfalfa Plants by Rhizobium leguminosarum biovar viciae1

    PubMed Central

    van Rhijn, Pieternel; Fujishige, Nancy A.; Lim, Pyung Ok; Hirsch, Ann M.

    2001-01-01

    Transgenic alfalfa (Medicago sativa L. cv Regen) roots carrying genes encoding soybean lectin or pea (Pisum sativum) seed lectin (PSL) were inoculated with Bradyrhizobium japonicum or Rhizobium leguminosarum bv viciae, respectively, and their responses were compared with those of comparably inoculated control plants. We found that nodule-like structures formed on alfalfa roots only when the rhizobial strains produced Nod factor from the alfalfa-nodulating strain, Sinorhizobium meliloti. Uninfected nodule-like structures developed on the soybean lectin-transgenic plant roots at very low inoculum concentrations, but bona fide infection threads were not detected even when B. japonicum produced the appropriate S. meliloti Nod factor. In contrast, the PSL-transgenic plants were not only well nodulated but also exhibited infection thread formation in response to R. leguminosarum bv viciae, but only when the bacteria expressed the complete set of S. meliloti nod genes. A few nodules from the PSL-transgenic plant roots were even found to be colonized by R. leguminosarum bv viciae expressing S. meliloti nod genes, but the plants were yellow and senescent, indicating that nitrogen fixation did not take place. Exopolysaccharide appears to be absolutely required for both nodule development and infection thread formation because neither occurred in PSL-transgenic plant roots following inoculation with an Exo− R. leguminosarum bv viciae strain that produced S. meliloti Nod factor. PMID:11351077

  14. Maize growth promotion by inoculation with Azospirillum brasilense and metabolites of Rhizobium tropici enriched on lipo-chitooligosaccharides (LCOs).

    PubMed

    Marks, Bettina Berquó; Megías, Manuel; Ollero, Francisco Javier; Nogueira, Marco Antonio; Araujo, Ricardo Silva; Hungria, Mariangela

    2015-12-01

    There is an increasing interest in the development and use of inoculants carrying plant growth-promoting bacteria (PGPB) in crops of agronomic interest. The great majority of the inoculants commercialized worldwide contain rhizobia for legume crops, but the use of PGPB as Azospirillum spp. for non-legume is expanding, as well as of inoculants combining microorganisms and microbial metabolites. In this study we evaluated the effects of inoculants containing Azospirillum brasilense with or without metabolites of Rhizobium tropici strain CIAT 899 highly enriched in lipo-chitooligosaccharides (LCOs) in six field experiments performed for three summer crop seasons in Brazil with maize (Zea mays L.). Inoculants and metabolites were applied either at sowing by seed inoculation, or by leaf spray at the V3 stage of plant growth. Improvement in shoot dry weight (SDW) and total N accumulated in shoots (TNS) by single, but especially by dual inoculation was observed in some of the experiments. Statistically significant increases in grain yield in relation to the non-inoculated control were observed in five out of six experiments when maize was inoculated with Azospirillum supplied with enriched metabolites of R. tropici applied by seed or leaf spray inoculation. The results give strength to the development of a new generation of inoculants carrying microorganisms and microbial molecules. PMID:26567001

  15. Inoculation of the nonlegume Capsicum annuum (L.) with Rhizobium strains. 1. Effect on bioactive compounds, antioxidant activity, and fruit ripeness.

    PubMed

    Silva, Luís R; Azevedo, Jessica; Pereira, Maria J; Carro, Lorena; Velazquez, Encarna; Peix, Alvaro; Valentão, Patrícia; Andrade, Paula B

    2014-01-22

    Pepper (Capsicum annuum L.) is an economically important agricultural crop and an excellent dietary source of natural colors and antioxidant compounds. The levels of these compounds can vary according to agricultural practices, like inoculation with plant growth-promoting rhizobacteria. In this work we evaluated for the first time the effect of the inoculation of two Rhizobium strains on C. annuum metabolites and bioactivity. The results revealed a decrease of organic acids and no effect on phenolics and capsaicinoids of leaves from inoculated plants. In the fruits from inoculated plants organic acids and phenolic compounds decreased, showing that fruits from inoculated plants present a higher ripeness stage than those from uninoculated ones. In general, the inoculation with Rhizobium did not improve the antioxidant activity of pepper fruits and leaves. Considering the positive effect on fruit ripening, the inoculation of C. annuum with Rhizobium is a beneficious agricultural practice for this nonlegume. PMID:24404842

  16. [Comparison of the adaptive potential for Rhizobium leguminosarum bv. viceae nodule bacterial populations isolated in natural ecosystems and agrocenoses].

    PubMed

    Kurchak, O N; Provorov, N A; Simarov, B V

    2011-04-01

    Polymorphism analysis was performed in Rhizobium leguminosarum bv. viceae populations isolated from geographically distant regions of Ukraine and Middle Asia. Examination of cultural, biochemical, and symbiotic traits revealed interpopulation differences, which were attributed to the difference in conditions between natural ecosystems and agrocenoses. Vetch has high species diversity and is not cultivated in Middle Asia, and the corresponding rhizobial population displayed higher genetic diversity and higher polymorphism of adaptive traits ensuring saprophytic development in soil and the rhizosphere, including melanin synthesis (35%) and active exopolysaccharide production (90%). Strains of the Ukrainian population had a lower exopolysaccharide production (10%), did not produce melanin, had higher herbicide resistance, and utilized glucose and succinate (main components of plant root exudation) as carbon sources. Strains capable of efficient symbiosis with Vicia villosa Roth. had a higher frequency in the Middle Asian than in the Ukrainian population, especially among strains isolated from soil (80 and 35%, respectively). In addition, strains of the Middle Asian population better competed for nodulation. It was assumed that the formation of rhizobial populations in vetch cultivation regions (Ukraine) is aimed at adaptation to ectosymbiotic (rhizospheric) interactions with plants and anthropogenic stress factors, while strains of the vetch original center (Middle Asia) are mostly adapted to the endosymbiotic interaction and to natural edaphic stress factors. PMID:21675237

  17. Relevance of Fucose-Rich Extracellular Polysaccharides Produced by Rhizobium sullae Strains Nodulating Hedysarum coronarium L. Legumes

    PubMed Central

    Carpéné, Marie-Anne; Couderc, François; Benguedouar, Ammar

    2013-01-01

    Specific and complex interactions between soil bacteria, known as rhizobia, and their leguminous host plants result in the development of root nodules. This process implies a complex dialogue between the partners. Rhizobia synthesize different classes of polysaccharides: exopolysaccharides (EPS), Kdo-rich capsular polysaccharides, lipopolysaccharides, and cyclic β-(1,2)-glucans. These polymers are actors of a successful symbiosis with legumes. We focus here on studying the EPS produced by Rhizobium sullae bacteria that nodulate Hedysarum coronarium L., largely distributed in Algeria. We describe the influence of the carbon source on the production and on the composition of EPS produced by R. sullae A6 and RHF strains. High-molecular-weight EPS preserve the bacteria from desiccation. The structural characterization of the EPS produced by R. sullae strains has been performed through sugar analysis by gas chromatography-mass spectrometry. The low-molecular-weight EPS of one strain (RHF) has been totally elucidated using nuclear magnetic resonance and quantitative time-of-flight tandem mass spectrometry analyses. An unusual fucose-rich EPS has been characterized. The presence of this deoxy sugar seems to be related to nodulation capacity. PMID:23183977

  18. Sinorhizobium fredii HH103 bacteroids are not terminally differentiated and show altered O-antigen in nodules of the Inverted Repeat-Lacking Clade legume Glycyrrhiza uralensis.

    PubMed

    Crespo-Rivas, Juan C; Guefrachi, Ibtissem; Mok, Kenny C; Villaécija-Aguilar, José A; Acosta-Jurado, Sebastián; Pierre, Olivier; Ruiz-Sainz, José E; Taga, Michiko E; Mergaert, Peter; Vinardell, José M

    2016-09-01

    In rhizobial species that nodulate inverted repeat-lacking clade (IRLC) legumes, such as the interaction between Sinorhizobium meliloti and Medicago, bacteroid differentiation is driven by an endoreduplication event that is induced by host nodule-specific cysteine rich (NCR) antimicrobial peptides and requires the participation of the bacterial protein BacA. We have studied bacteroid differentiation of Sinorhizobium fredii HH103 in three host plants: Glycine max, Cajanus cajan and the IRLC legume Glycyrrhiza uralensis. Flow cytometry, microscopy analyses and viability studies of bacteroids as well as confocal microscopy studies carried out in nodules showed that S. fredii HH103 bacteroids, regardless of the host plant, had deoxyribonucleic acid (DNA) contents, cellular sizes and survival rates similar to those of free-living bacteria. Contrary to S. meliloti, S. fredii HH103 showed little or no sensitivity to Medicago NCR247 and NCR335 peptides. Inactivation of S. fredii HH103 bacA neither affected symbiosis with Glycyrrhiza nor increased bacterial sensitivity to Medicago NCRs. Finally, HH103 bacteroids isolated from Glycyrrhiza, but not those isolated from Cajanus or Glycine, showed an altered lipopolysaccharide. Our studies indicate that, in contrast to the S. meliloti-Medicago model symbiosis, bacteroids in the S. fredii HH103-Glycyrrhiza symbiosis do not undergo NCR-induced and bacA-dependent terminal differentiation. PMID:26521863

  19. Efficient utilization of complex N-linked glycans is a selective advantage for Bacteroides fragilis in extraintestinal infections

    PubMed Central

    Cao, Yanlu; Rocha, Edson R.; Smith, C. Jeffrey

    2014-01-01

    Bacteroides fragilis is the most common anaerobe isolated from clinical infections, and in this report we demonstrate a characteristic of the species that is critical to their success as an opportunistic pathogen. Among the Bacteroides spp. in the gut, B. fragilis has the unique ability of efficiently harvesting complex N-linked glycans from the glycoproteins common to serum and serous fluid. This activity is mediated by an outer membrane protein complex designated as Don. Using the abundant serum glycoprotein transferrin as a model, it has been shown that B. fragilis alone can rapidly and efficiently deglycosylate this protein in vitro and that transferrin glycans can provide the sole source of carbon and energy for growth in defined media. We then showed that transferrin deglycosylation occurs in vivo when B. fragilis is propagated in the rat tissue cage model of extraintestinal growth, and that this ability provides a competitive advantage in vivo over strains lacking the don locus. PMID:25139987

  20. Mutation of the Zinc-Binding Metalloprotease Motif Affects Bacteroides fragilis Toxin Activity but Does Not Affect Propeptide Processing

    PubMed Central

    Franco, Augusto A.; Buckwold, Simy L.; Shin, Jai W.; Ascon, Miguel; Sears, Cynthia L.

    2005-01-01

    To evaluate the role of the zinc-binding metalloprotease in Bacteroides fragilis toxin (BFT) processing and activity, the zinc-binding consensus sequences (H348, E349, H352, G355, H358, and M366) were mutated by site-directed-mutagenesis. Our results indicated that single point mutations in the zinc-binding metalloprotease motif do not affect BFT processing but do reduce or eliminate BFT biologic activity in vitro. PMID:16041055

  1. First national survey of antibiotic susceptibility of the Bacteroides fragilis group: emerging resistance to carbapenems in Argentina.

    PubMed

    Fernández-Canigia, Liliana; Litterio, Mirta; Legaria, María C; Castello, Liliana; Predari, Silvia C; Di Martino, Ana; Rossetti, Adelaida; Rollet, Raquel; Carloni, Graciela; Bianchini, Hebe; Cejas, Daniela; Radice, Marcela; Gutkind, Gabriel

    2012-03-01

    The antibiotic susceptibility rates of 363 clinical Bacteroides fragilis group isolates collected from 17 centers in Argentina during the period from 2006 to 2009 were as follows: piperacillin-tazobactam, 99%; ampicillin-sulbactam, 92%; cefoxitin, 72%; tigecycline, 100%; moxifloxacin, 91%; and clindamycin, 52%. No metronidazole resistance was detected in these isolates during this time period. Resistance to imipenem, doripenem, and ertapenem was observed in 1.1%, 1.6%, and 2.3% of B. fragilis group strains, respectively. B. fragilis species showed a resistance profile of 1.5% to imipenem, 1.9% to doripenem, and 2.4% to ertapenem. This is the first report of carbapenem resistance in Argentina. The cfiA gene was present in 8 out of 23 isolates, all of them belonging to the B. fragilis species and displaying reduced susceptibility or resistance to carbapenems (MICs ≥ 4 μg/ml). Three out of eight cfiA-positive isolates were fully resistant to carbapenems, while 5 out of 8 isolates showed low-level resistance (MICs, 4 to 8 μg/ml). The inhibition by EDTA was a good predictor of the presence of metallo-β-lactamases in the fully resistant B. fragilis strains, but discrepant results were observed for low-level resistant isolates. B. fragilis was more susceptible to antimicrobial agents than other Bacteroides species. Bacteroides vulgatus species was the most resistant to ampicillin-sulbactam and piperacillin-tazobactam, and B. thetaiotaomicron/ovatus strains showed the highest level of resistance to carbapenems, with an unknown resistance mechanism. B. vulgatus and the uncommon non-Bacteroides fragilis species were the most resistant to moxifloxacin, showing an overall resistance rate of 15.1%. PMID:22232282

  2. Competitive PCR for Quantitation of a Cytophaga-Flexibacter-Bacteroides Phylum Bacterium Associated with the Tuber borchii Vittad. Mycelium

    PubMed Central

    Barbieri, Elena; Riccioni, Giulia; Pisano, Anna; Sisti, Davide; Zeppa, Sabrina; Agostini, Deborah; Stocchi, Vilberto

    2002-01-01

    An uncultured bacterium associated with the ectomycorrhizal fungus Tuber borchii Vittad. was identified as a novel member of the Cytophaga-Flexibacter-Bacteroides group. Utilizing a quantitative PCR targeting the 16S rRNA gene, we relatively quantified this bacterium in the host. The estimated number of bacteria was found to be approximately 106 cells per 30-day-old T. borchii mycelium culture. This represents the first molecular attempt to enumerate an uncultured bacterium associated with a mycorrhizal fungus. PMID:12450871

  3. The symbiotic defect of Rhizobium meliloti exopolysaccharide mutants is suppressed by lpsZ sup + , a gene involved in lipopolysaccharide biosynthesis

    SciTech Connect

    Williams, M.N.V.; Klein, S.; Signer, E.R. ); Hollingsworth, R.I. )

    1990-05-01

    exo mutants of Rhizobium meliloti SU47, which fail to secrete acidic extracellular polysaccharide (EPS), induce Fix{sup {minus}} nodules on alfalfa. However, mutants of R. meliloti Rm41 carrying the same exo lesions induce normal Fix{sup +} nodules. The authors show that such induction is due to a gene from strain Rm41, which they call lpsZ{sup +}, that is missing in strain SU47. lpsZ{sup +} does not restore EPS production but instead alters the composition an structure of lipopolysaccharide. In both SU47 and Rm41, either lpsZ{sup +} or exo{sup +} is sufficient for normal nodulation. This suggests that in R. meliloti EPS and lipopolysaccharide can perform the same function in nodule development.

  4. Use of abundance ratios of somatic coliphages and bacteriophages of Bacteroides thetaiotaomicron GA17 for microbial source identification.

    PubMed

    Muniesa, Maite; Lucena, Francisco; Blanch, Anicet R; Payán, Andrey; Jofre, Juan

    2012-12-01

    Water contaminated with human faeces is a risk to human health and management of water bodies can be improved by determining the sources of faecal pollution. Field studies show that existing methods are insufficient and that different markers are required. This study proposes the combined use of two microbial indicators, the concentrations of which are presented as ratios. This provides a more reliable approach to identifying faecal sources as it avoids variation due to treatment or ageing of the contamination. Among other indicators, bacteriophages have been proposed as rapid and cheap indicators of faecal pollution. Samples analysed in this study were derived from wastewater treatment plants (raw sewage, secondary and tertiary effluents and raw sewage sludge) river water, seawater and animal related wastewater. The abundance ratios of faecal coliforms and Bacteroides phages, either strain RYC2056 (non-specific for faecal origin) or strain GA17 (specific for human pollution), and among somatic coliphages and phages infecting both Bacteroides strains, were evaluated. The results indicate that the ratio of somatic coliphages and phages infecting Bacteroides strain GA17, which is specific to human faecal sources, provides a robust method for discriminating samples, even those presenting different levels and ages of pollution, and allows samples polluted with human faeces to be distinguished from those containing animal faecal pollution. This method allows the generation of numerical data that can be further applied to numerical methods for faecal pollution discrimination. PMID:23039916

  5. Effects of decomposing rice straw on growth of and nitrogen fixation by Rhizobium

    SciTech Connect

    Rice, E.L.; Huang, C.Y.; Lin, C.Y.

    1981-03-01

    Five phenolic compounds produced in decomposing rice straw and sterile extracts of decomposing rice straw in soil were very inhibitory to growth of three strains of Rhizobium. The effects were additive and in several instances synergistic. The phenolic compounds also reduced nodule numbers and hemoglobin content of the nodules in two bean (Phaseohus vulgaris) varieties. Extracts of decomposing rice straw in soil (same concentration as in the soil) significantly reduced N/sub 2/ fixation (acetylene reduction) in Bush Black Seeded beans. This may explain in part the great reduction in soybean yields in Taiwan following rice crops when the rice stubble is left in the field.

  6. DNA, a possible site of action of aluminum in Rhizobium spp

    SciTech Connect

    Johnson, A.C.; Wood, M. )

    1990-12-01

    Al was found to penetrate the cell envelopes of both sensitive and tolerant Rhizobium strains and bind to DNA in vivo. Despite causing a reduction viability, Al stimulated DNA synthesis in the sensitive strain, which suggested that an excision repair mechanism was operating. The Al-stimulated DNA synthesis was reduced by the simultaneous addition of chloramphenicol. In contrast to the sensitive strain, DNA synthesis was unaffected by Al binding to DNA in the tolerant strain. It is proposed that Al enters the cell and binds to the DNA helix, increasing stabilization and preventing successful replication. Different repair mechanisms appear to operate in response to Al in tolerant and sensitive strains.

  7. Rhizobium meliloti chromosomal loci required for suppression of exopolysaccharide mutations by lipopolysaccharide

    SciTech Connect

    Williams, M.N.V.; Brzoska, P.M.; Signer, E.R. ); Hollingsworth, R.I. )

    1990-11-01

    Mutants of alfalfa symbiont Rhizobium meliloti SU47 that fail to make extracellular polysaccharide (exo mutants) induce the formation of nodules that are devoid of bacteria and consequently do not fix nitrogen. This Fix{sup {minus}} phenotype can be suppressed by an R. meliloti Rm41 gene that affects lipopolysaccharide structure. Here we describe mutations preventing suppression that map at two new chromosomal loci, lpsY and lpsX, present in both strains. Two other lps mutations isolated previously from SU47 also prevented suppression.

  8. Arbuscular mycorrhizal fungi and rhizobium facilitate nitrogen uptake and transfer in soybean/maize intercropping system

    PubMed Central

    Meng, Lingbo; Zhang, Aiyuan; Wang, Fei; Han, Xiaoguang; Wang, Dejiang; Li, Shumin

    2015-01-01

    The tripartite symbiosis between legumes, rhizobia and mycorrhizal fungi are generally considered to be beneficial for the nitrogen (N) uptake of legumes, but the facilitation of symbiosis in legume/non-legume intercropping systems is not clear. Therefore, the aims of the research are as follows: (1) to verify if the dual inoculation can facilitate the N uptake and N transfer in maize/soybean intercropping systems and (2) to calculate how much N will be transferred from soybean to maize. A pot experiment with different root separations [solid barrier, mesh (30 μm) barrier and no barrier] was conducted, and the 15N isotopic tracing method was used to calculate how much N transferred from soybean to maize inoculated with arbuscular mycorrhizal fungi (AMF) and rhizobium in a soybean (Glycine max L.cv. Dongnong No. 42)/maize (Zea mays L.cv. Dongnong No. 48) intercropping system. Compared with the Glomus mosseae inoculation (G.m.), Rhizobium SH212 inoculation (SH212), no inoculation (NI), the dual inoculation (SH212+G.m.) increased the N uptake of soybean by 28.69, 39.58, and 93.07% in a solid barrier system. N uptake of maize inoculated with both G. mosseae and rhizobium was 1.20, 1.28, and 1.68 times more than that of G.m., SH212 and NI, respectively, in solid barrier treatments. In addition, the amount of N transferred from soybean to maize in a dual inoculation system with a mesh barrier was 7.25, 7.01, and 11.45 mg more than that of G.m., SH212 and NI and similarly, 6.40, 7.58, and 12.46 mg increased in no barrier treatments. Inoculating with both AMF and rhizobium in the soybean/maize intercropping system improved the N fixation efficiency of soybean and promoted N transfer from soybean to maize, resulting in the improvement of yield advantages of legume/non-legume intercropping. PMID:26029236

  9. l-2-Haloacid dehalogenase (DehL) from Rhizobium sp. RC1.

    PubMed

    Adamu, Aliyu; Wahab, Roswanira Abdul; Huyop, Fahrul

    2016-01-01

    l-2-Haloacid dehalogenase (DehL) from Rhizobium sp. RC1 is a stereospecific enzyme that acts exclusively on l-isomers of 2-chloropropionate and dichloroacetate. The amino acid sequence of this enzyme is substantially different from those of other l-specific dehalogenases produced by other organisms. DehL has not been crystallised, and hence its three-dimensional structure is unavailable. Herein, we review what is known concerning DehL and tentatively identify the amino acid residues important for catalysis based on a comparative structural and sequence analysis with well-characterised l-specific dehalogenases. PMID:27347470

  10. Proteins Exported via the PrsD-PrsE Type I Secretion System and the Acidic Exopolysaccharide Are Involved in Biofilm Formation by Rhizobium leguminosarum

    PubMed Central

    Russo, Daniela M.; Williams, Alan; Edwards, Anne; Posadas, Diana M.; Finnie, Christine; Dankert, Marcelo; Downie, J. Allan; Zorreguieta, Angeles

    2006-01-01

    The type I protein secretion system of Rhizobium leguminosarum bv. viciae encoded by the prsD and prsE genes is responsible for secretion of the exopolysaccharide (EPS)-glycanases PlyA and PlyB. The formation of a ring of biofilm on the surface of the glass in shaken cultures by both the prsD and prsE secretion mutants was greatly affected. Confocal laser scanning microscopy analysis of green-fluorescent-protein-labeled bacteria showed that during growth in minimal medium, R. leguminosarum wild type developed microcolonies, which progress to a characteristic three-dimensional biofilm structure. However, the prsD and prsE secretion mutants were able to form only an immature biofilm structure. A mutant disrupted in the EPS-glycanase plyB gene showed altered timing of biofilm formation, and its structure was atypical. A mutation in an essential gene for EPS synthesis (pssA) or deletion of several other pss genes involved in EPS synthesis completely abolished the ability of R. leguminosarum to develop a biofilm. Extracellular complementation studies of mixed bacterial cultures confirmed the role of the EPS and the modulation of the biofilm structure by the PrsD-PrsE secreted proteins. Protein analysis identified several additional proteins secreted by the PrsD-PrsE secretion system, and N-terminal sequencing revealed peptides homologous to the N termini of proteins from the Rap family (Rhizobium adhering proteins), which could have roles in cellular adhesion in R. leguminosarum. We propose a model for R. leguminosarum in which synthesis of the EPS leads the formation of a biofilm and several PrsD-PrsE secreted proteins are involved in different aspects of biofilm maturation, such as modulation of the EPS length or mediating attachment between bacteria. PMID:16740954

  11. Purification of pili from Bacteroides nodosus and an examination of their chemical, physical and serological properties.

    PubMed

    Every, D

    1979-12-01

    Pili from Bacteroides nodosus were purified to greater than 99% homogeneity by precipitation at pH 4.0 and in MgCl2 followed by chromatography on BioGel A150. The pili were composed entirely of one type of polypeptide subunit, pilin. No carbohydrates, nucleic acid, lipid, lipopolysaccharide or phosphate could be detected in purified pili preparations. The molecular weight of pilin from B. nodosus strains 91B and 198 was 18,400 and from strain 80 was 19,300. The isoelectric points of pili from B. nodosus strains 91B and 80 were both 4.5. The buoyant densities of pili from strains 91B, 80 and 198 were 1.287, 1.284 and 1.286 g ml-1, respectively. The three strains of B. nodosus did not cross-react in K-agglutination tests and produced pili which did not cross-react in immunodiffusion tests. Antiserum to highly purified pili caused a characteristic K-type agglutination reaction. It was concluded that pili are the K-agglutinogen. PMID:43354

  12. The Bacteroides sp. 3_1_23 Pif1 protein is a multifunctional helicase.

    PubMed

    Liu, Na-Nv; Duan, Xiao-Lei; Ai, Xia; Yang, Yan-Tao; Li, Ming; Dou, Shuo-Xing; Rety, Stephane; Deprez, Eric; Xi, Xu-Guang

    2015-10-15

    ScPif1 DNA helicase is the prototypical member of a 5'-to-3' helicase superfamily conserved from bacteria to human and plays various roles in the maintenance of genomic homeostasis. While many studies have been performed with eukaryotic Pif1 helicases, including yeast and human Pif1 proteins, the potential functions and biochemical properties of prokaryotic Pif1 helicases remain largely unknown. Here, we report the expression, purification and biochemical analysis of Pif1 helicase from Bacteroides sp. 3_1_23 (BsPif1). BsPif1 binds to a large panel of DNA substrates and, in particular, efficiently unwinds partial duplex DNAs with 5'-overhang, fork-like substrates, D-loop and flap-like substrates, suggesting that BsPif1 may act at stalled DNA replication forks and enhance Okazaki fragment maturation. Like its eukaryotic homologues, BsPif1 resolves R-loop structures and unwinds DNA-RNA hybrids. Furthermore, BsPif1 efficiently unfolds G-quadruplexes and disrupts nucleoprotein complexes. Altogether, these results highlight that prokaryotic Pif1 helicases may resolve common issues that arise during DNA transactions. Interestingly, we found that BsPif1 is different from yeast Pif1, but resembles more human Pif1 with regard to substrate specificity, helicase activity and mode of action. These findings are discussed in the context of the possible functions of prokaryotic Pif1 helicases in vivo. PMID:26384418

  13. Structural and functional diversity of metalloproteinases encoded by the Bacteroides fragilis pathogenicity island

    PubMed Central

    Shiryaev, Sergey A.; Aleshin, Alexander E.; Muranaka, Norihito; Kukreja, Muskan; Routenberg, David A.; Remacle, Albert G.; Liddington, Robert C.; Cieplak, Piotr; Kozlov, Igor A.; Strongin, Alex Y.

    2014-01-01

    Summary Bacteroides fragilis causes the majority of anaerobic infections in humans. The presence of a pathogenicity island in the genome discriminates pathogenic and commensal B. fragilis strains. The island encodes metalloproteinase II (MPII), a potential virulence protein, and one of three homologous fragilysin isozymes (FRA; also termed B. fragilis toxin or BFT). Here, we report biochemical data on the structural-functional characteristics of the B. fragilis pathogenicity island proteases by reporting the crystal structure of MPII at 2.13 Å resolution combined with detailed characterization of the cleavage preferences of MPII and FRA3 (as a representative of the FRA isoforms) identified using a high-throughput peptide cleavage assay with 18,583 substrate peptides. We suggest that the evolution of the MPII catalytic domain can be traced to human and archaebacterial proteinases, while the prodomain fold is a feature specific to MPII and FRA. We conclude that the catalytic domain of both MPII and FRA3 evolved differently relative to the prodomain, and that the prodomain evolved specifically to fit the B. fragilis pathogenicity. Overall, our data provide insights into the evolution of cleavage specificity and activation mechanisms in the virulent metalloproteinases. PMID:24698179

  14. Cloning and sequencing of a Bacteroides ruminicola B(1)4 endoglucanase gene.

    PubMed Central

    Matsushita, O; Russell, J B; Wilson, D B

    1990-01-01

    Bacteroides ruminicola B(1)4, a noncellulolytic rumen bacterium, produces an endoglucanase (carboxymethylcellulase [CMCase]) that is excreted into the culture supernatant. Cultures grown on glucose, fructose, maltose, mannose, and cellobiose had high specific activities of CMCase (greater than 3 mmol of reducing sugar per mg of protein per min), but its synthesis was repressed by sucrose. B. rumincola did not grow on either ball-milled or acid-swollen cellulose even though the CMCase could hydrolyze swollen cellulose. The CMCase gene was cloned into Escherichia coli, and its nucleotide sequence contained a single open reading frame coding for a protein of 40,481 daltons. The enzyme was overproduced in E. coli under the control of the tac promoter and purified to homogeneity. The N-terminal sequence, amino acid composition, and molecular weight of the purified enzyme were similar to the values predicted from the open reading frame of the DNA sequence. However, the CMCase present in B. ruminicola was found to have a monomer molecular weight of 88,000 by Western immunoblotting. This discrepancy appeared to have resulted from our having cloned only part of the CMCase gene into E. coli. The amino acid sequence of the CMCase showed homology to sequences of beta-glucanases from Ruminococcus albus and Clostridium thermocellum. Images PMID:2361940

  15. Anti-stress proteins produced by Bacteroides thetaiotaomicron after nutrient starvation.

    PubMed

    Hochart-Behra, Anne-Cécile; Drobecq, Hervé; Tourret, Mélissa; Dubreuil, Luc; Behra-Miellet, Josette

    2014-08-01

    Bacteroides thetaiotaomicron maybe one of the most adaptable intestinal bacteria due to its complex genome. Known to be an opportunistic pathogenic anaerobe, B. thetaiotaomicron has recently been described as a symbiont with anti-inflammatory properties. In this study, peptide mass finger printing technique was used to identify the stress proteins (maybe anti-stress proteins for the host) extracted from B. thetaiotaomicron grown under nutrient starvation (without heme, blood or bile) prior to be placed in an aerobic solution containing a mild non-ionic detergent derived from cholic acid. We focus here on proteins related to stress, knowing that superoxide dismutase was previously identified in the extract. In parallel, the morphology of the bacterial cells was observed using electronic microscopy before and after the extraction process. The effective antioxidant effect of the extract was evaluated in vitro against hydrogen peroxide. This work highlights the B. thetaiotaomicron ability to produce a large amount of stress proteins and to remain viable during the extraction. Budding vesicles were observed on its cell wall. The extraction process did not exceed 20 h in order to preserve the bacterial viability that decreased significantly after 24 h in preliminary studies. In our experimental conditions, an inhibitory effect of the extract was found against hydrogen peroxide. Animal models of inflammation will later check in vivo if this extract of anti-stress proteins is able to counter the respiratory burst beginning an inflammation process. PMID:24785350

  16. Levan Enhances Associated Growth of Bacteroides, Escherichia, Streptococcus and Faecalibacterium in Fecal Microbiota

    PubMed Central

    Adamberg, Kaarel; Tomson, Katrin; Talve, Tiina; Pudova, Ksenia; Puurand, Marju; Visnapuu, Triinu; Alamäe, Tiina; Adamberg, Signe

    2015-01-01

    The role of dietary fiber in supporting healthy gut microbiota and overall well-being of the host has been revealed in several studies. Here, we show the effect of a bacterial polyfructan levan on the growth dynamics and metabolism of fecal microbiota in vitro by using isothermal microcalorimetry. Eleven fecal samples from healthy donors were incubated in phosphate-buffered defined medium with or without levan supplementation and varying presence of amino acids. The generation of heat, changes in pH and microbiota composition, concentrations of produced and consumed metabolites during the growth were determined. The composition of fecal microbiota and profile of metabolites changed in response to substrate (levan and amino acids) availability. The main products of levan metabolism were acetic, lactic, butyric, propionic and succinic acids and carbon dioxide. Associated growth of levan-degrading (e.g. Bacteroides) and butyric acid-producing (e.g. Faecalibacterium) taxa was observed in levan-supplemented media. The study shows that the capacity of levan and possibly also other dietary fibers/prebiotics to modulate the composition and function of colon microbiota can be predicted by using isothermal microcalorimetry of fecal samples linked to metabolite and consortia analyses. PMID:26629816

  17. Metabolism of a 5-nitroimidazole in susceptible and resistant isogenic strains of Bacteroides fragilis.

    PubMed Central

    Carlier, J P; Sellier, N; Rager, M N; Reysset, G

    1997-01-01

    We investigated the metabolism of dimetridazole (1,2-dimethyl-5-nitroimidazole) (DMZ) by the resting cell method in a susceptible strain of Bacteroides fragilis and in the same strain containing the nimA gene, which conferred resistance to 5-nitroimidazole drugs. In both cases, under strict anaerobic conditions DMZ was metabolized without major ring cleavage or nitrate formation. However, one of two distinct metabolic pathways is involved, depending on the susceptibility of the strain. In the susceptible strain, the classical reduction pathway of nitroaromatic compounds is followed at least as far as the nitroso-radical anion, with further formation of the azo-dimer: 5,5'-azobis-(1,2-dimethylimidazole). In the resistant strain, DMZ is reduced to the amine derivative, namely, 5-amino-1,2-dimethylimidazole, preventing the formation of the toxic form of the drug. The specificity of the six-electron reduction of the nitro group, which is restricted to 4- and 5-nitroimidazole, suggests an enzymatic reaction. We thus conclude that nimA and related genes may encode a 5-nitroimidazole reductase. PMID:9210672

  18. Suggested alternative starch utilization system from the human gut bacterium Bacteroides thetaiotaomicron.

    PubMed

    Chaudet, Marcia M; Rose, David R

    2016-06-01

    The human digestive system is host to a highly populated ecosystem of bacterial species that significantly contributes to our assimilation of dietary carbohydrates. Bacteroides thetaiotaomicron is a member of this ecosystem, and participates largely in the role of the gut microbiome by breaking down dietary complex carbohydrates. This process of acquiring glycans from the colon lumen is predicted to rely on the mechanisms of proteins that are part of a classified system known as polysaccharide utilization loci (PUL). These loci are responsible for binding substrates at the cell outer membrane, internalizing them, and then hydrolyzing them within the periplasm into simple sugars. Here we report our investigation into specific components of a PUL, and suggest an alternative starch utilization system in B. thetaiotaomicron. Our analysis of an outer membrane binding protein, a SusD homolog, highlights its contribution to this PUL by acquiring starch-based sugars from the colon lumen. Through our structural characterization of two Family GH31 α-glucosidases, we reveal the flexibility of this bacterium with respect to utilizing a range of starch-derived glycans with an emphasis on branched substrates. With these results we demonstrate the predicted function of a gene locus that is capable of contributing to starch hydrolysis in the human colon. PMID:27093479

  19. Two new xylanases with different substrate specificities from the human gut bacterium Bacteroides intestinalis DSM 17393.

    PubMed

    Hong, Pei-Ying; Iakiviak, Michael; Dodd, Dylan; Zhang, Meiling; Mackie, Roderick I; Cann, Isaac

    2014-04-01

    Xylan is an abundant plant cell wall polysaccharide and is a dominant component of dietary fiber. Bacteria in the distal human gastrointestinal tract produce xylanase enzymes to initiate the degradation of this complex heteropolymer. These xylanases typically derive from glycoside hydrolase (GH) families 10 and 11; however, analysis of the genome sequence of the xylan-degrading human gut bacterium Bacteroides intestinalis DSM 17393 revealed the presence of two putative GH8 xylanases. In the current study, we demonstrate that the two genes encode enzymes that differ in activity. The xyn8A gene encodes an endoxylanase (Xyn8A), and rex8A encodes a reducing-end xylose-releasing exo-oligoxylanase (Rex8A). Xyn8A hydrolyzed both xylopentaose (X5) and xylohexaose (X6) to a mixture of xylobiose (X2) and xylotriose (X3), while Rex8A hydrolyzed X3 through X6 to a mixture of xylose (X1) and X2. Moreover, rex8A is located downstream of a GH3 gene (xyl3A) that was demonstrated to exhibit β-xylosidase activity and would be able to further hydrolyze X2 to X1. Mutational analyses of putative active site residues of both Xyn8A and Rex8A confirm their importance in catalysis by these enzymes. Recent genome sequences of gut bacteria reveal an increase in GH8 Rex enzymes, especially among the Bacteroidetes, indicating that these genes contribute to xylan utilization in the human gut. PMID:24463968

  20. Structural dissection of a complex Bacteroides ovatus gene locus conferring xyloglucan metabolism in the human gut

    PubMed Central

    Thompson, Andrew J.; Stepper, Judith; Sobala, Łukasz F.; Coyle, Travis; Larsbrink, Johan; Spadiut, Oliver; Goddard-Borger, Ethan D.; Stubbs, Keith A.; Brumer, Harry; Davies, Gideon J.

    2016-01-01

    The human gastrointestinal tract harbours myriad bacterial species, collectively termed the microbiota, that strongly influence human health. Symbiotic members of our microbiota play a pivotal role in the digestion of complex carbohydrates that are otherwise recalcitrant to assimilation. Indeed, the intrinsic human polysaccharide-degrading enzyme repertoire is limited to various starch-based substrates; more complex polysaccharides demand microbial degradation. Select Bacteroidetes are responsible for the degradation of the ubiquitous vegetable xyloglucans (XyGs), through the concerted action of cohorts of enzymes and glycan-binding proteins encoded by specific xyloglucan utilization loci (XyGULs). Extending recent (meta)genomic, transcriptomic and biochemical analyses, significant questions remain regarding the structural biology of the molecular machinery required for XyG saccharification. Here, we reveal the three-dimensional structures of an α-xylosidase, a β-glucosidase, and two α-l-arabinofuranosidases from the Bacteroides ovatus XyGUL. Aided by bespoke ligand synthesis, our analyses highlight key adaptations in these enzymes that confer individual specificity for xyloglucan side chains and dictate concerted, stepwise disassembly of xyloglucan oligosaccharides. In harness with our recent structural characterization of the vanguard endo-xyloglucanse and cell-surface glycan-binding proteins, the present analysis provides a near-complete structural view of xyloglucan recognition and catalysis by XyGUL proteins. PMID:27466444

  1. Isolation and some properties of exohemagglutinin from the culture medium of Bacteroides gingivalis 381.

    PubMed Central

    Inoshita, E; Amano, A; Hanioka, T; Tamagawa, H; Shizukuishi, S; Tsunemitsu, A

    1986-01-01

    Exohemagglutinin was found in the culture medium of Bacteroides gingivalis 381. Exohemagglutinin was purified 3,150-fold from culture fluid by ultracentrifugation followed by gel filtration on Sepharose CL-4B and by affinity chromatography on arginine-agarose. Examination of the final preparation of exohemagglutinin by biochemical analysis and sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed that the isolated exohemagglutinin contained three major proteins but not a detectable lipopolysaccharide. Hemagglutination inhibition experiments showed that the activity of exohemagglutinin was inhibited by L-arginine and the arginine-containing peptides, although the activity was unaffected by the sugars tested. Some protein and glycoproteins that were examined also exhibited the inhibitory activity. When the bovine submaxillary mucin was chemically modified by beta-elimination and bovine serum albumin was modified by guanidination, the inhibitory effects on hemagglutination were significantly enhanced. These results suggest that the hemagglutination of the isolated exohemagglutinin may be involved in arginine residues as components of ligand-binding sites on erythrocytes. Images PMID:3699890

  2. Bacteroides fragilis enterotoxin induces cytoskeletal changes and surface blebbing in HT-29 cells.

    PubMed Central

    Donelli, G; Fabbri, A; Fiorentini, C

    1996-01-01

    Certain strains of the anaerobic bacterium Bacteroides fragilis are known to produce an enterotoxin of about 20 kDa which is able to induce a fluid response in ligated intestinal loops and a cytotoxic response in HT-29 cells. It presents protease activity, belonging to a family of metalloproteases termed metzincins. In order to investigate the mode of action of the enterotoxin in cultured cells, we performed a study with HT-29 cells, using both fluoresence and electron microscopy. Treated cells underwent morphological changes, mainly consisting of the retraction of the cell body and the formation of numerous blebs on the cell surface. The microfilament system was reorganized, the F-actin being condensed as a ring at the cell periphery, whereas other cell organelles appeared to be unaffected. All these changes, clearly visible after 3 h of exposure to the toxin, were reversed within 24 h of treatment. By inhibiting the protease activity of the toxin with specific metal chelators, the cytoskeletal effects were also prevented. Thus, B. fragilis enterotoxin appears to act on cells by reversibly modifying the actin cytoskeleton, an effect probably dependent on its proteolytic activity. PMID:8557328

  3. Effects of Carbon Dioxide on Growth and Maltose Fermentation by Bacteroides amylophilus

    PubMed Central

    Caldwell, Daniel R.; Keeney, Mark; Van Soest, Peter J.

    1969-01-01

    The requirement of carbon dioxide for growth of Bacteroides amylophilus is quantitatively similar to that of certain other rumen bacteria. Carbon dioxide could be replaced by bicarbonate, but not by formate or certain amino acids. Label from 14CO2 was incorporated into the succinate produced during maltose fermentation by B. amylophilus, and during glucose fermentation by B. ruminicola, and during cellobiose fermentation by B. succinogenes. All of the incorporated label could be associated with the carboxyl function of the molecule. The depression in radioactivity per micromole of carbon in the succinate formed from the fermentation of uniformly labeled 14C-maltose by B. amylophilus was greater than would be expected if all of the succinate formed was produced via a direct CO2 fixation pathway(s) involving phosphoenolpyruvate or pyruvate; the radioactivity per micromole of carbon suggests that as much as 60% of the total succinate results from a pathway(s) involving direct CO2 fixation. Maltose fermentation by B. amylophilus was dependent upon CO2 concentration, but CO2 concentration could not be shown to influence either the fermentation end-product ratios or the proportion of total succinate formed attributable to CO2 fixation. PMID:5814705

  4. Detection, identification, and comparison of Capnocytophaga, Bacteroides ochraceus, and DF-1.

    PubMed Central

    Newman, M G; Sutter, V L; Pickett, M J; Blachman, U; Greenwood, J R; Grinenko, V; Citron, D

    1979-01-01

    Working independently, three laboratories had recognized considerable similarity among certain strains of dysgonic, fermentative, capnophilic, surface translocating, gram-negative bacilli referred to as Capnocytophaga, Bacteroides ochraceus, and Center for Disease Control biogroup DF-1. To determine the relationship among these groups, 21 strains were exchanged and independently characterized by the three laboratories. Additionally, a fourth laboratory examined the deoxyribonucleic acid homologies of the same strains. Using methods common to dental microbiology, eight of the strains had been isolated from the gingival sulcus and periodontal lesions and identified as Capnocytophaga. Three strains isolated from blood and transtracheal aspirate had been characterized by conventional anaerobic methods and recorded as B. ochraceus. Ten strains isolated from sputum, blood, throat, spinal fluid, and tracheal aspirate had been identified as DF-1 with the methods of E. O. King and a buffered single-substrate technique. All strains were similar in respect to colonial and microscopic morphology, surface translocation, biochemical features, gas-liquid chromatograms of metabolic end products, and deoxyribonucleic acid composition. We conclude that these biogroups should be termed Capnocytophaga species. Images PMID:528686

  5. Structural and functional diversity of metalloproteinases encoded by the Bacteroides fragilis pathogenicity island.

    PubMed

    Shiryaev, Sergey A; Aleshin, Alexander E; Muranaka, Norihito; Kukreja, Muskan; Routenberg, David A; Remacle, Albert G; Liddington, Robert C; Cieplak, Piotr; Kozlov, Igor A; Strongin, Alex Y

    2014-06-01

    Bacteroides fragilis causes the majority of anaerobic infections in humans. The presence of a pathogenicity island in the genome discriminates pathogenic and commensal B. fragilis strains. The island encodes metalloproteinase II (MPII), a potential virulence protein, and one of three homologous fragilysin isozymes (FRA; also termed B. fragilis toxin or BFT). Here, we report biochemical data on the structural-functional characteristics of the B. fragilis pathogenicity island proteases by reporting the crystal structure of MPII at 2.13 Å resolution, combined with detailed characterization of the cleavage preferences of MPII and FRA3 (as a representative of the FRA isoforms), identified using a high-throughput peptide cleavage assay with 18 583 substrate peptides. We suggest that the evolution of the MPII catalytic domain can be traced to human and archaebacterial proteinases, whereas the prodomain fold is a feature specific to MPII and FRA. We conclude that the catalytic domain of both MPII and FRA3 evolved differently relative to the prodomain, and that the prodomain evolved specifically to fit the B. fragilis pathogenicity. Overall, our data provide insights into the evolution of cleavage specificity and activation mechanisms in the virulent metalloproteinases. PMID:24698179

  6. Levan Enhances Associated Growth of Bacteroides, Escherichia, Streptococcus and Faecalibacterium in Fecal Microbiota.

    PubMed

    Adamberg, Kaarel; Tomson, Katrin; Talve, Tiina; Pudova, Ksenia; Puurand, Marju; Visnapuu, Triinu; Alamäe, Tiina; Adamberg, Signe

    2015-01-01

    The role of dietary fiber in supporting healthy gut microbiota and overall well-being of the host has been revealed in several studies. Here, we show the effect of a bacterial polyfructan levan on the growth dynamics and metabolism of fecal microbiota in vitro by using isothermal microcalorimetry. Eleven fecal samples from healthy donors were incubated in phosphate-buffered defined medium with or without levan supplementation and varying presence of amino acids. The generation of heat, changes in pH and microbiota composition, concentrations of produced and consumed metabolites during the growth were determined. The composition of fecal microbiota and profile of metabolites changed in response to substrate (levan and amino acids) availability. The main products of levan metabolism were acetic, lactic, butyric, propionic and succinic acids and carbon dioxide. Associated growth of levan-degrading (e.g. Bacteroides) and butyric acid-producing (e.g. Faecalibacterium) taxa was observed in levan-supplemented media. The study shows that the capacity of levan and possibly also other dietary fibers/prebiotics to modulate the composition and function of colon microbiota can be predicted by using isothermal microcalorimetry of fecal samples linked to metabolite and consortia analyses. PMID:26629816

  7. Differential proteomic analysis of outer membrane enriched extracts of Bacteroides fragilis grown under bile salts stress.

    PubMed

    Boente, Renata F; Pauer, Heidi; Silva, Deborah N S; Filho, Joaquim Santos; Sandim, Vanessa; Antunes, Luis Caetano M; Ferreira, Rosana Barreto Rocha; Zingali, Russolina B; Domingues, Regina M C P; Lobo, Leandro A

    2016-06-01

    Bacteroides fragilis is the most commonly isolated anaerobic bacteria from infectious processes. Several virulence traits contribute to the pathogenic nature of this bacterium, including the ability to tolerate the high concentrations of bile found in the gastrointestinal tract (GIT). The activity of bile salts is similar to detergents and may lead to membrane permeabilization and cell death. Modulation of outer membrane proteins (OMPs) is considered a crucial event to bile salts resistance. The primary objective of the current work was to identify B. fragilis proteins associated with the stress induced by high concentration of bile salts. The outer membrane of B. fragilis strain 638R was isolated after growth either in the presence of 2% conjugated bile salts or without bile salts. The membrane fractions were separated on SDS-PAGE and analyzed by ESI-Q/TOF tandem mass spectrometry. A total of 37 proteins were identified; among them nine were found to be expressed exclusively in the absence of bile salts whereas eight proteins were expressed only in the presence of bile salts. These proteins are related to cellular functions such as transport through membrane, nutrient uptake, and protein-protein interactions. This study demonstrates the alteration of OMPs composition in B. fragilis during bile salts stress resistance and adaptation to environmental changes. Proteomics of OMPs was also shown to be a useful approach in the identification of new targets for functional analyses. PMID:26948242

  8. Location and characteristics of enzymes involved in the breakdown of polygalacturonic acid by Bacteroides thetaiotaomicron.

    PubMed Central

    McCarthy, R E; Kotarski, S F; Salyers, A A

    1985-01-01

    When Bacteroides thetaiotaomicron is grown in medium which contains polygalacturonic acid (PGA) as the sole carbon source, two different polygalacturonases are produced: a PGA lyase (EC 4.2.2.2) and a PGA hydrolase (EC 3.2.1.15). Both enzymes are cell associated. The PGA hydrolase appears to be an inner membrane protein. The PGA lyase is a soluble protein that associates with membranes under certain conditions. The PGA lyase was purified to apparent homogeneity. It has a molecular weight (from sodium dodecyl sulfate-polyacrylamide gel electrophoresis) of 74,000, a pH optimum of 8.7, a pI of 7.5, and a Km for PGA of 40 to 70 micrograms/ml. It requires calcium for maximal activity. The main product of this enzyme appears to be a disaccharide that contains a delta 4,5-unsaturated galacturonic acid residue. The PGA hydrolase can be solubilized from membranes with 2% Triton X-100 and has been partially purified. It has a pH optimum of 5.4 to 5.5, a pI of 4.7 to 4.9, and a Km for PGA of 350 to 400 micrograms/ml. The main product of this enzyme appears to be galacturonic acid. The specific activities of both PGA hydrolase and PGA lyase increase at the same rate when bacteria are exposed to PGA. The two enzymes therefore appear to be similarly regulated. Images PMID:3968032

  9. Structural dissection of a complex Bacteroides ovatus gene locus conferring xyloglucan metabolism in the human gut.

    PubMed

    Hemsworth, Glyn R; Thompson, Andrew J; Stepper, Judith; Sobala, Łukasz F; Coyle, Travis; Larsbrink, Johan; Spadiut, Oliver; Goddard-Borger, Ethan D; Stubbs, Keith A; Brumer, Harry; Davies, Gideon J

    2016-07-01

    The human gastrointestinal tract harbours myriad bacterial species, collectively termed the microbiota, that strongly influence human health. Symbiotic members of our microbiota play a pivotal role in the digestion of complex carbohydrates that are otherwise recalcitrant to assimilation. Indeed, the intrinsic human polysaccharide-degrading enzyme repertoire is limited to various starch-based substrates; more complex polysaccharides demand microbial degradation. Select Bacteroidetes are responsible for the degradation of the ubiquitous vegetable xyloglucans (XyGs), through the concerted action of cohorts of enzymes and glycan-binding proteins encoded by specific xyloglucan utilization loci (XyGULs). Extending recent (meta)genomic, transcriptomic and biochemical analyses, significant questions remain regarding the structural biology of the molecular machinery required for XyG saccharification. Here, we reveal the three-dimensional structures of an α-xylosidase, a β-glucosidase, and two α-l-arabinofuranosidases from the Bacteroides ovatus XyGUL. Aided by bespoke ligand synthesis, our analyses highlight key adaptations in these enzymes that confer individual specificity for xyloglucan side chains and dictate concerted, stepwise disassembly of xyloglucan oligosaccharides. In harness with our recent structural characterization of the vanguard endo-xyloglucanse and cell-surface glycan-binding proteins, the present analysis provides a near-complete structural view of xyloglucan recognition and catalysis by XyGUL proteins. PMID:27466444

  10. Nucleotide sequence of the gene encoding the two-subunit pilin of Bacteroides nodosus 265.

    PubMed Central

    Elleman, T C; Hoyne, P A; McKern, N M; Stewart, D J

    1986-01-01

    The nucleotide sequence of the gene encoding pilin from Bacteroides nodosus 265 has been determined. The pilin is encoded by a single-copy gene, from which can be predicted a prepilin comprising a single protein chain of Mr 16,637. The prepilin sequence differs in several respects from the mature protein sequence. Seven additional N-terminal amino acid residues are present in prepilin, whereas residue 8, phenylalanine, undergoes posttranslational modification to become the N-methylated amino-terminal residue of mature pilin. In addition, further processing occurs through internal cleavage to produce two noncovalently linked subunits characteristic of pilins from serogroup H of B. nodosus, of which strain 265 is a member. The position of cleavage has been identified between alanine residues at positions 72 and 73 of the mature 149-residue pilin protein. The predicted pilin sequence of B. nodosus 265 shows extensive N-terminal amino acid sequence homology with other pilins of the N-methylphenylalanine type. In addition this sequence also shows homology with these N-methylphenylalanine-type pilins in the C-terminal region of the molecule, especially with pilin from Pseudomonas aeruginosa PAK. Images PMID:2873127

  11. A Scaffoldin of the Bacteroides cellulosolvens Cellulosome That Contains 11 Type II Cohesins

    PubMed Central

    Ding, Shi-You; Bayer, Edward A.; Steiner, David; Shoham, Yuval; Lamed, Raphael

    2000-01-01

    A cellulosomal scaffoldin gene, termed cipBc, was identified and sequenced from the mesophilic cellulolytic anaerobe Bacteroides cellulosolvens. The gene encodes a 2,292-residue polypeptide (excluding the signal sequence) with a calculated molecular weight of 242,437. CipBc contains an N-terminal signal peptide, 11 type II cohesin domains, an internal family III cellulose-binding domain (CBD), and a C-terminal dockerin domain. Its CBD belongs to family IIIb, like that of CipV from Acetivibrio cellulolyticus but unlike the family IIIa CBDs of other clostridial scaffoldins. In contrast to all other scaffoldins thus far described, CipBc lacks a hydrophilic domain or domain X of unknown function. The singularity of CipBc, however, lies in its numerous type II cohesin domains, all of which are very similar in sequence. One of the latter cohesin domains was expressed, and the expressed protein interacted selectively with cellulosomal enzymes, one of which was identified as a family 48 glycosyl hydrolase on the basis of partial sequence alignment. By definition, the dockerins, carried by the cellulosomal enzymes of this species, would be considered to be type II. This is the first example of authentic type II cohesins that are confirmed components of a cellulosomal scaffoldin subunit rather than a cell surface anchoring component. The results attest to the emerging diversity of cellulosomes and their component sequences in nature. PMID:10940036

  12. Differential Metabolism of Exopolysaccharides from Probiotic Lactobacilli by the Human Gut Symbiont Bacteroides thetaiotaomicron

    PubMed Central

    Saraf, Aakanksha; Martens, Eric C.; Dijkhuizen, Lubbert

    2015-01-01

    Probiotic microorganisms are ingested as food or supplements and impart positive health benefits to consumers. Previous studies have indicated that probiotics transiently reside in the gastrointestinal tract and, in addition to modulating commensal species diversity, increase the expression of genes for carbohydrate metabolism in resident commensal bacterial species. In this study, it is demonstrated that the human gut commensal species Bacteroides thetaiotaomicron efficiently metabolizes fructan exopolysaccharide (EPS) synthesized by probiotic Lactobacillus reuteri strain 121 while only partially degrading reuteran and isomalto/malto-polysaccharide (IMMP) α-glucan EPS polymers. B. thetaiotaomicron metabolized these EPS molecules via the activation of enzymes and transport systems encoded by dedicated polysaccharide utilization loci specific for β-fructans and α-glucans. Reduced metabolism of reuteran and IMMP α-glucan EPS molecules may be due to reduced substrate binding by components of the starch utilization system (sus). This study reveals that microbial EPS substrates activate genes for carbohydrate metabolism in B. thetaiotaomicron and suggests that microbially derived carbohydrates provide a carbohydrate-rich reservoir for B. thetaiotaomicron nutrient acquisition in the gastrointestinal tract. PMID:25841008

  13. Isolation, Detection, and Characterization of Enterotoxigenic Bacteroides fragilis in Clinical Samples

    PubMed Central

    Fathi, Payam; Wu, Shaoguang

    2016-01-01

    Bacteroides fragilis is an extensively studied anaerobic bacterium comprising the normal flora of the human gut. B. fragilis is known to be one of the most commonly isolated species from clinical samples and has been shown to cause a wide range of pathologies in humans [1, 2]. As an opportunistic pathogen B. fragilis can cause abscess formation and bacteremia [2]. Additionally in its enterotoxigenic form, B. fragilis is a known cause of diarrheal illness, is associated with inflammatory bowel disease, and has been recently characterized in patients with colon cancer [3 - 5]. As research in the field of the gut microbiome continues to expand at an ever increasing rate due to advances in the availability of next generation sequencing and analysis tools it is important to outline various molecular methods that can be employed in quickly detecting and isolating relevant strains of B. fragilis. This review outlines methods that are routinely employed in the isolation and detection of B. fragilis, with an emphasis on characterizing enterotoxigenic B. fragilis (ETBF) strains. PMID:27335618

  14. Multidomain Carbohydrate-binding Proteins Involved in Bacteroides thetaiotaomicron Starch Metabolism*

    PubMed Central

    Cameron, Elizabeth A.; Maynard, Mallory A.; Smith, Christopher J.; Smith, Thomas J.; Koropatkin, Nicole M.; Martens, Eric C.

    2012-01-01

    Human colonic bacteria are necessary for the digestion of many dietary polysaccharides. The intestinal symbiont Bacteroides thetaiotaomicron uses five outer membrane proteins to bind and degrade starch. Here, we report the x-ray crystallographic structures of SusE and SusF, two outer membrane proteins composed of tandem starch specific carbohydrate-binding modules (CBMs) with no enzymatic activity. Examination of the two CBMs in SusE and three CBMs in SusF reveals subtle differences in the way each binds starch and is reflected in their Kd values for both high molecular weight starch and small maltooligosaccharides. Thus, each site seems to have a unique starch preference that may enable these proteins to interact with different regions of starch or its breakdown products. Proteins similar to SusE and SusF are encoded in many other polysaccharide utilization loci that are possessed by human gut bacteria in the phylum Bacteroidetes. Thus, these proteins are likely to play an important role in carbohydrate metabolism in these abundant symbiotic species. Understanding structural changes that diversify and adapt related proteins in the human gut microbial community will be critical to understanding the detailed mechanistic roles that they perform in the complex digestive ecosystem. PMID:22910908

  15. Pyogenic arthritis of native joints due to Bacteroides fragilis: Case report and review of the literature.

    PubMed

    Nolla, Joan M; Murillo, Oscar; Narvaez, Javier; Vaquero, Carmen Gómez; Lora-Tamayo, Jaime; Pedrero, Salvador; Cabo, Javier; Ariza, Javier

    2016-06-01

    Pyogenic arthritis of native joints due to Bacteroides fragilis seems to be an infrequent disease. We analyzed the cases diagnosed in a tertiary hospital during a 22-year period and reviewed the literature to summarize the experience with this infectious entity.In our institution, of 308 patients with pyogenic arthritis of native joints, B fragilis was the causative organism in 2 (0.6%) cases. A MEDLINE search (1981-2015) identified 19 additional cases.Of the 21 patients available for review (13 men and 8 women, with a mean age, of 54.4 ± 17 years), 19 (90%) presented a systemic predisposing factor for infection; the most common associated illness was rheumatoid arthritis (8 patients). Bacteremia was documented in 65% (13/20) of cases. In 5 patients (24%), 1 or more concomitant infectious process was found. Metronidazole was the most frequently used antibiotic. Surgical drainage was performed in 11 cases (52%). The overall mortality rate was 5%.Pyogenic arthritis of native joints due to B fragilis is an infrequent disease that mainly affects elderly patients with underlying medical illnesses and in whom bacteremia and the presence of a concomitant infectious process are frequent conditions. PMID:27336895

  16. Differential Metabolism of Exopolysaccharides from Probiotic Lactobacilli by the Human Gut Symbiont Bacteroides thetaiotaomicron.

    PubMed

    Lammerts van Bueren, Alicia; Saraf, Aakanksha; Martens, Eric C; Dijkhuizen, Lubbert

    2015-06-15

    Probiotic microorganisms are ingested as food or supplements and impart positive health benefits to consumers. Previous studies have indicated that probiotics transiently reside in the gastrointestinal tract and, in addition to modulating commensal species diversity, increase the expression of genes for carbohydrate metabolism in resident commensal bacterial species. In this study, it is demonstrated that the human gut commensal species Bacteroides thetaiotaomicron efficiently metabolizes fructan exopolysaccharide (EPS) synthesized by probiotic Lactobacillus reuteri strain 121 while only partially degrading reuteran and isomalto/malto-polysaccharide (IMMP) α-glucan EPS polymers. B. thetaiotaomicron metabolized these EPS molecules via the activation of enzymes and transport systems encoded by dedicated polysaccharide utilization loci specific for β-fructans and α-glucans. Reduced metabolism of reuteran and IMMP α-glucan EPS molecules may be due to reduced substrate binding by components of the starch utilization system (sus). This study reveals that microbial EPS substrates activate genes for carbohydrate metabolism in B. thetaiotaomicron and suggests that microbially derived carbohydrates provide a carbohydrate-rich reservoir for B. thetaiotaomicron nutrient acquisition in the gastrointestinal tract. PMID:25841008

  17. RapA2 Is a Calcium-binding Lectin Composed of Two Highly Conserved Cadherin-like Domains That Specifically Recognize Rhizobium leguminosarum Acidic Exopolysaccharides*

    PubMed Central

    Abdian, Patricia L.; Caramelo, Julio J.; Ausmees, Nora; Zorreguieta, Angeles

    2013-01-01

    In silico analyses have revealed a conserved protein domain (CHDL) widely present in bacteria that has significant structural similarity to eukaryotic cadherins. A CHDL domain was shown to be present in RapA, a protein that is involved in autoaggregation of Rhizobium cells, biofilm formation, and adhesion to plant roots as shown by us and others. Structural similarity to cadherins suggested calcium-dependent oligomerization of CHDL domains as a mechanistic basis for RapA action. Here we show by circular dichroism spectroscopy, light scattering, isothermal titration calorimetry, and other methods that RapA2 from Rhizobium leguminosarum indeed exhibits a cadherin-like β-sheet conformation and that its proper folding and stability are dependent on the binding of one calcium ion per protein molecule. By further in silico analysis we also reveal that RapA2 consists of two CHDL domains and expand the range of CHDL-containing proteins in bacteria and archaea. However, light scattering assays at various concentrations of added calcium revealed that RapA2 formed neither homo-oligomers nor hetero-oligomers with RapB (a distinct CHDL protein), indicating that RapA2 does not mediate cellular interactions through a cadherin-like mechanism. Instead, we demonstrate that RapA2 interacts specifically with the acidic exopolysaccharides (EPSs) produced by R. leguminosarum in a calcium-dependent manner, sustaining a role of these proteins in the development of the biofilm matrix made of EPS. Because EPS binding by RapA2 can only be attributed to its two CHDL domains, we propose that RapA2 is a calcium-dependent lectin and that CHDL domains in various bacterial and archaeal proteins confer carbohydrate binding activity to these proteins. PMID:23235153

  18. Epitope identification for a panel of anti-Sinorhizobium meliloti monoclonal antibodies and application to the analysis of K antigens and lipopolysaccharides from bacteroids

    SciTech Connect

    Reuhs, B.L.; Stephens, S.B.; Geller, D.P.; Kim, J.S.; Glenn, J.; Przytycki, J.; Ojanen-Reuhs, T.

    1999-11-01

    In two published reports using monoclonal antibodies (MAbs) generated against whole cells, Olsen et al. showed that strain-specific antigens on the surface of cultured cells of Sinorhyzobium meliloti were diminished or absent in the endophytic cells (bacteroids) recovered from alfalfa nodules, whereas two common antigens were not affected by bacterial differentiation. The nature of the antigens, however, were not determined in those studies. For this report, the epitopes for five of the anti-S. meliloti MAbs were identified by polyacrylamide gel electrophoresis-immunoblot analyses of the polysaccharides extracted from S. meliloti and Sinorhizobium fridii. This showed that the strain-specific MAbs recognized K antigens, whereas the strain-cross-reactive MAbs recognized the lipopolysaccharide (LPS) core. The MAbs were then used in the analysis of the LPS and K antigens extracted from S. meliloti bacteroids, which had been recovered from the root nodules of alfalfa, and the results supported the findings of Olsen et al. The size range of the K antigens from bacteroids of S. meliloti NRG247 on polyacrylamide gels was altered, and the epitope was greatly diminished in abundance compared to those from the cultured cells, and no K antigens were detected in the S. meliloti NRG185 bacteroid extract. In contrast to the K antigens, the LPS core appeared to be similar in both cultured cells and bacteroids, although a higher proportion of the LPS fractionated into the organic phase during the phenol-water extraction of the bacteroid polysaccharides. Importantly, immunoblot analysis with an anti-LPS MAb showed that smooth LPS production was modified in the bacteroids.

  19. Population genomics of the symbiotic plasmids of sympatric nitrogen-fixing Rhizobium species associated with Phaseolus vulgaris.

    PubMed

    Pérez Carrascal, Olga M; VanInsberghe, David; Juárez, Soledad; Polz, Martin F; Vinuesa, Pablo; González, Víctor

    2016-09-01

    Cultivated common beans are the primary protein source for millions of people around the world who subsist on low-input agriculture, enabled by the symbiotic N2 -fixation these legumes perform in association with rhizobia. Within a single agricultural plot, multiple Rhizobium species can nodulate bean roots, but it is unclear how genetically isolated these species remain in sympatry. To better understand this issue, we sequenced and compared the genomes of 33 strains isolated from the rhizosphere and root nodules of a particular bean variety grown in the same agricultural plot. We found that the Rhizobium species we observed coexist with low genetic recombination across their core genomes. Accessory plasmids thought to be necessary for the saprophytic lifestyle in soil show similar levels of genetic isolation, but with higher rates of recombination than the chromosomes. However, the symbiotic plasmids are extremely similar, with high rates of recombination and do not appear to have co-evolved with the chromosome or accessory plasmids. Therefore, while Rhizobium species are genetically isolated units within the microbial community, a common symbiotic plasmid allows all Rhizobium species to engage in symbiosis with the same host in a single agricultural plot. PMID:27312778

  20. Applying Reversible Mutations of Nodulation and Nitrogen-Fixation Genes to Study Social Cheating in Rhizobium etli-Legume Interaction

    PubMed Central

    Wang, Hui; Zhong, Zengtao; Zhu, Jun

    2013-01-01

    Mutualisms are common in nature, though these symbioses can be quite permeable to cheaters in situations where one individual parasitizes the other by discontinuing cooperation yet still exploits the benefits of the partnership. In the Rhizobium-legume system, there are two separate contexts, namely nodulation and nitrogen fixation processes, by which resident Rhizobium individuals can benefit by cheating. Here, we constructed reversible and irreversible mutations in key nodulation and nitrogen-fixation pathways of Rhizobium etli and compared their interaction with plant hosts Phaseolus vulgaris to that of wild type. We show that R. etli reversible mutants deficient in nodulation factor production are capable of intra-specific cheating, wherein mutants exploit other Rhizobium individuals capable of producing these factors. Similarly, we show that R. etli mutants are also capable of cheating inter-specifically, colonizing the host legume yet contributing nothing to the partnership in terms of nitrogen fixation. Our findings indicate that cheating is possible in both of these frameworks, seemingly without damaging the stability of the mutualism itself. These results may potentially help explain observations suggesting that legume plants are commonly infected by multiple bacterial lineages during the nodulation process. PMID:23922937

  1. Rhizobium qilianshanense sp. nov., a novel species isolated from root nodule of Oxytropis ochrocephala Bunge in China.

    PubMed

    Xu, Lin; Zhang, Yong; Deng, Zheng Shan; Zhao, Liang; Wei, Xiu Li; Wei, Ge Hong

    2013-03-01

    During a study of the diversity and phylogeny of rhizobia isolated from root nodules of Oxytropis ochrocephala grown in the northwest of China, four strains were classified in the genus Rhizobium on the basis of their 16S rRNA gene sequences. These strains have identical 16S rRNA gene sequences, which showed a mean similarity of 94.4 % with the most closely related species, Rhizobium oryzae. Analysis of recA and glnA sequences showed that these strains have less than 88.1 and 88.7 % similarity with the defined species of Rhizobium, respectively. The genetic diversity revealed by ERIC-PCR fingerprinting indicated that the isolates correspond to different strains. Strain CCNWQLS01(T) contains Q-10 as the predominant ubiquinone. The major fatty acids were identified as feature 8 (C18: 1ω7c and/or C18: 1ω6c; 67.2 %). Therefore, a novel species Rhizobium qilianshanense sp. nov. is proposed, and CCNWQLS01(T) (= ACCC 05747(T) = JCM 18337(T)) is designated as the type strain. PMID:23142858

  2. Extended region of nodulation genes in Rhizobium meliloti 1021. I. Phenotypes of Tn5 insertion mutants

    SciTech Connect

    Swanson, J.A.; Tu, J.K.; Ogawa, J.; Sanga, R.; Fisher, R.F.; Long, S.R.

    1987-10-01

    Rhizobium meliloti Nod/sup -/ mutant WL131, a derivative of wild-type strain 102F51, was complemented by a clone bank of wild-type R. meliloti 1021 DNA, and clone pRmJT5 was recovered. Transfer of pRmJT5 conferred alfalfa nodulation on other Rhizobium species, indicating a role in host range determination for pRmJT5. Mutagenesis of pRmJT5 revealed several segments in which transposon insertion causes delay in nodulation, and/or marked reduction of the number of nodules formed on host alfalfa plants. The set of mutants indicated five regions in which nod genes are located; one mutant, nod-216, is located in a region not previously reported to encode a nodulation gene. Other mutant phenotypes correlated with the positions of open reading frames for nodH, nodF and nodE, and with a 2.2-kb EcoRI fragment. A mutant in nodG had no altered phenotype in this strain. One nodulation mutant was shown to be a large deletion of the common nod gene region. The authors present a discussion comparing the various studies made on this extended nod gene region.

  3. Production of Proteasome Inhibitor Syringolin A by the Endophyte Rhizobium sp. Strain AP16

    PubMed Central

    Bigler, Laurent; Dudler, Robert

    2014-01-01

    Syringolin A, the product of a mixed nonribosomal peptide synthetase/polyketide synthase encoded by the syl gene cluster, is a virulence factor secreted by certain Pseudomonas syringae strains. Together with the glidobactins produced by a number of beta- and gammaproteobacterial human and animal pathogens, it belongs to the syrbactins, a structurally novel class of proteasome inhibitors. In plants, proteasome inhibition by syringolin A-producing P. syringae strains leads to the suppression of host defense pathways requiring proteasome activity, such as the ones mediated by salicylic acid and jasmonic acid. Here we report the discovery of a syl-like gene cluster with some unusual features in the alphaproteobacterial endophyte Rhizobium sp. strain AP16 that encodes a putative syringolin A-like synthetase whose components share 55% to 65% sequence identity (72% to 79% similarity) at the amino acid level. As revealed by average nucleotide identity (ANI) calculations, this strain likely belongs to the same species as biocontrol strain R. rhizogenes K84 (formely known as Agrobacterium radiobacter K84), which, however, carries a nonfunctional deletion remnant of the syl-like gene cluster. Here we present a functional analysis of the syl-like gene cluster of Rhizobium sp. strain AP16 and demonstrate that this endophyte synthesizes syringolin A and some related minor variants, suggesting that proteasome inhibition by syrbactin production can be important not only for pathogens but also for endophytic bacteria in the interaction with their hosts. PMID:24727275

  4. Synthesis of glycerophosphorylated cyclic beta-(1,2)-glucans by Rhizobium meliloti ndv mutants.

    PubMed Central

    Breedveld, M W; Yoo, J S; Reinhold, V N; Miller, K J

    1994-01-01

    The periplasmic cyclic beta-(1,2)-glucans of Rhizobium spp. are believed to provide functions during hypoosmotic adaptation and legume nodulation. In Rhizobium meliloti, cyclic beta-(1,2)-glucans are synthesized at highest levels when cells are grown at low osmolarity, and a considerable fraction (> or = 35%) of these glucans may become substituted with phosphoglycerol moieties. Thus far, two chromosomally encoded proteins, NdvA and NdvB, have been shown to function during cyclic beta-(1,2)-glucan biosynthesis; however, the precise roles for these proteins remain unclear. In the present study, we show that R. meliloti mutants lacking up to one-third of the downstream region of ndvB synthesize cyclic beta-(1,2)-glucans similar to those produced by wild-type cells with respect to size and phosphoglycerol substituent profile. In contrast, no phosphoglycerol substituents were detected on the cyclic beta-(1,2)-glucans synthesized by an R. meliloti ndvA mutant. PMID:8106315

  5. Performance of fenugreek bioinoculated with Rhizobium meliloti strains under semi-arid condition.

    PubMed

    Singh, N K; Patel, D B

    2016-01-01

    Rhizobium meliloti strains were isolated from the fields of S.D. Agricultural University (Gujarat, India) and were maintained in the Congo Red Yeast Extract Mannitol Agar medium. These strains were tested for their effectiveness for fenugreek crop grown under semi-arid condition. Among the six Rhizobium strains, FRS-7 strain showed best plant growth parameters like shoot length, shoot dry weight, shoot total nitrogen, root length, root dry weight, root total nitrogen, seed yield, 1000 grain weight, number of root nodules, and nodules fresh and dry weight. The performance of this strain was better as compared to 20 kgN ha(-1) treatment through urea and was even far better over control plot. Seed yields obtained with FRS-7 during two years were 10.14 and 9.66 q ha(-1); which was about 36.8% and 45.9% high over control. This strain resulted in saving of about 20 kgN ha(-1) accompanied with better crop yield and soil health. Results of the present experiments can be utilized in integrated nutrient management for cultivation of fenugreek in semi-arid areas to provide sustainability to agricultural productivity in such regions. PMID:26930857

  6. Industrial wastewater as raw material for exopolysaccharide production by Rhizobium leguminosarum.

    PubMed

    Sellami, Mohamed; Oszako, Tomasz; Miled, Nabil; Ben Rebah, Faouzi

    2015-06-01

    The objective of this study was to evaluate the exopolysaccharide (EPS) production by Rhizobium leguminosarum cultivated in wastewater generated by oil companies (WWOC1 and WWOC2) and fish processing industry (WWFP). The results obtained in Erlenmeyer flasks indicated that the rhizobial strain grew well in industrial wastewater. Generally, wastewater composition affected the growth and the EPS production. WWFP allowed good bacterial growth similar to that obtained with the standard medium (YMB). During growth, various quantities of EPS were produced and yields varied depending on the media. Growing in YMB, EPS production did not exceed 9.7 g/L obtained after 72 h of growth. In wastewater, the maximum EPS value reached 11.1 g/L obtained with the fish processing wastewater, after 72 h of growth. The use of a mixture of the oil company wastewater (WWOC2) and the fish processing wastewater (WWFP) as culture medium affected not only the rhizobial strain growth, but also EPS production. The highest EPS (42.4 g/L, after 96 h of culture) was obtained using a ratio of WWFP and WWOC2 of 50:50 (v:v). Therefore, this work shows the ability of Rhizobium leguminosarum, growing in industrial wastewater as new economic medium, to produce EPS. This biopolymer could be applied in enormous biotechnological areas. PMID:26273255

  7. Rhizobium-Legume Symbiosis and Nitrogen Fixation under Severe Conditions and in an Arid Climate

    PubMed Central

    Zahran, Hamdi Hussein

    1999-01-01

    Biological N2 fixation represents the major source of N input in agricultural soils including those in arid regions. The major N2-fixing systems are the symbiotic systems, which can play a significant role in improving the fertility and productivity of low-N soils. The Rhizobium-legume symbioses have received most attention and have been examined extensively. The behavior of some N2-fixing systems under severe environmental conditions such as salt stress, drought stress, acidity, alkalinity, nutrient deficiency, fertilizers, heavy metals, and pesticides is reviewed. These major stress factors suppress the growth and symbiotic characteristics of most rhizobia; however, several strains, distributed among various species of rhizobia, are tolerant to stress effects. Some strains of rhizobia form effective (N2-fixing) symbioses with their host legumes under salt, heat, and acid stresses, and can sometimes do so under the effect of heavy metals. Reclamation and improvement of the fertility of arid lands by application of organic (manure and sewage sludge) and inorganic (synthetic) fertilizers are expensive and can be a source of pollution. The Rhizobium-legume (herb or tree) symbiosis is suggested to be the ideal solution to the improvement of soil fertility and the rehabilitation of arid lands and is an important direction for future research. PMID:10585971

  8. Novel organization of the common nodulation genes in Rhizobium leguminosarum bv. phaseoli strains.

    PubMed Central

    Vázquez, M; Dávalos, A; de las Peñas, A; Sánchez, F; Quinto, C

    1991-01-01

    Nodulation by Rhizobium, Bradyrhizobium, and Azorhizobium species in the roots of legumes and nonlegumes requires the proper expression of plant genes and of both common and specific bacterial nodulation genes. The common nodABC genes form an operon or are physically mapped together in all species studied thus far. Rhizobium leguminosarum bv. phaseoli strains are classified in two groups. The type I group has reiterated nifHDK genes and a narrow host range of nodulation. The type II group has a single copy of the nifHDK genes and a wide host range of nodulation. We have found by genetic and nucleotide sequence analysis that in type I strain CE-3, the functional common nodA gene is separated from the nodBC genes by 20 kb and thus is transcriptionally separated from the latter genes. This novel organization could be the result of a complex rearrangement, as we found zones of identity between the two separated nodA and nodBC regions. Moreover, this novel organization of the common nodABC genes seems to be a general characteristic of R. leguminosarum bv. phaseoli type I strains. Despite the separation, the coordination of the expression of these genes seems not to be altered. PMID:1991718

  9. Isolation and characterization of an early colonizing Rhizobium sp. R8 from a household toilet bowl.

    PubMed

    Fukano, Toru; Gomi, Mitsuhiro; Osaki, Yukihiko; Morikawa, Masaaki

    2015-01-01

    The bacterial community structure was compared between the third days', one week', and three weeks' biofilm samples from the surface of a household toilet bowl. It was found that the PCR-DGGE band pattern of 16S rRNA gene was dramatically changed after the third day and was not further changed until three weeks. This result suggests that there are early and late colonizing bacterial groups. One of the early colonizers isolated from the third days' sample was Rhizobium sp. R8, a closest relative to Rhizobium giardinii, which exhibited the highest biofilm formation activity in an artificial urine condition. R8 produced extracellular polysaccharides containing galactose, glucose, and mannose at the molar ratio of 8:1:1, which were probably responsible for the biofilm formation. Its excelled biofilm formation and urease activities together with the lack of nodulation and nitrogen fixing genes in R8 suggest that this strain has been specifically adapted to urine condition in a toilet bowl. PMID:25707633

  10. Industrial wastewater as raw material for exopolysaccharide production by Rhizobium leguminosarum

    PubMed Central

    Sellami, Mohamed; Oszako, Tomasz; Miled, Nabil; Ben Rebah, Faouzi

    2015-01-01

    The objective of this study was to evaluate the exopolysaccharide (EPS) production by Rhizobium leguminosarum cultivated in wastewater generated by oil companies (WWOC1 and WWOC2) and fish processing industry (WWFP). The results obtained in Erlenmeyer flasks indicated that the rhizobial strain grew well in industrial wastewater. Generally, wastewater composition affected the growth and the EPS production. WWFP allowed good bacterial growth similar to that obtained with the standard medium (YMB). During growth, various quantities of EPS were produced and yields varied depending on the media. Growing in YMB, EPS production did not exceed 9.7 g/L obtained after 72 h of growth. In wastewater, the maximum EPS value reached 11.1 g/L obtained with the fish processing wastewater, after 72 h of growth. The use of a mixture of the oil company wastewater (WWOC2) and the fish processing wastewater (WWFP) as culture medium affected not only the rhizobial strain growth, but also EPS production. The highest EPS (42.4 g/L, after 96 h of culture) was obtained using a ratio of WWFP and WWOC2 of 50:50 (v:v). Therefore, this work shows the ability of Rhizobium leguminosarum, growing in industrial wastewater as new economic medium, to produce EPS. This biopolymer could be applied in enormous biotechnological areas. PMID:26273255

  11. Prebiotic Effects of Wheat Arabinoxylan Related to the Increase in Bifidobacteria, Roseburia and Bacteroides/Prevotella in Diet-Induced Obese Mice

    PubMed Central

    Neyrinck, Audrey M.; Possemiers, Sam; Druart, Céline; Van de Wiele, Tom; De Backer, Fabienne; Cani, Patrice D.; Larondelle, Yvan; Delzenne, Nathalie M.

    2011-01-01

    Background Alterations in the composition of gut microbiota - known as dysbiosis - has been proposed to contribute to the development of obesity, thereby supporting the potential interest of nutrients targeting the gut with beneficial effect for host adiposity. We test the ability of a specific concentrate of water-extractable high molecular weight arabinoxylans (AX) from wheat to modulate both the gut microbiota and lipid metabolism in high-fat (HF) diet-induced obese mice. Methodology/Principal Findings Mice were fed either a control diet (CT) or a HF diet, or a HF diet supplemented with AX (10% w/w) during 4 weeks. AX supplementation restored the number of bacteria that were decreased upon HF feeding, i.e. Bacteroides-Prevotella spp. and Roseburia spp. Importantly, AX treatment markedly increased caecal bifidobacteria content, in particular Bifidobacterium animalis lactis. This effect was accompanied by improvement of gut barrier function and by a lower circulating inflammatory marker. Interestingly, rumenic acid (C18:2 c9,t11) was increased in white adipose tissue due to AX treatment, suggesting the influence of gut bacterial metabolism on host tissue. In parallel, AX treatment decreased adipocyte size and HF diet-induced expression of genes mediating differentiation, fatty acid uptake, fatty acid oxidation and inflammation, and decreased a key lipogenic enzyme activity in the subcutaneous adipose tissue. Furthermore, AX treatment significantly decreased HF-induced adiposity, body weight gain, serum and hepatic cholesterol accumulation and insulin resistance. Correlation analysis reveals that Roseburia spp. and Bacteroides/Prevotella levels inversely correlate with these host metabolic parameters. Conclusions/Significance Supplementation of a concentrate of water-extractable high molecular weight AX in the diet counteracted HF-induced gut dysbiosis together with an improvement of obesity and lipid-lowering effects. We postulate that hypocholesterolemic, anti

  12. Loss of NHE3 alters gut microbiota composition and influences Bacteroides thetaiotaomicron growth

    PubMed Central

    Engevik, Melinda A.; Aihara, Eitaro; Montrose, Marshall H.; Shull, Gary E.; Hassett, Daniel J.

    2013-01-01

    Changes in the intestinal microbiota have been linked to diabetes, obesity, inflammatory bowel disease, and Clostridium difficile (C. difficile)-associated disease. Despite this, it remains unclear how the intestinal environment, set by ion transport, affects luminal and mucosa-associated bacterial composition. Na+/H+-exchanger isoform 3 (NHE3), a target of C. difficile toxin B, plays an integral role in intestinal Na+ absorption. Thus the NHE3-deficient mouse model was chosen to examine the effect of pH and ion composition on bacterial growth. We hypothesized that ion transport-induced change in the intestinal environment would lead to alteration of the microbiota. Region-specific changes in ion composition and pH correlated with region-specific alteration of luminal and mucosal-associated bacteria with general decreases in Firmicutes and increases in Bacteroidetes members. Bacteroides thetaiotaomicron (B. thetaiotaomicron) increased in NHE3−/− terminal ileum and was examined in vitro to determine whether altered Na+ was sufficient to affect growth. Increased in vitro growth of B. thetaiotaomicron occurred in 43 mM Na+ correlating with the NHE3−/− mouse terminal ileum [Na+]. NHE3−/− terminal ileum displayed increased fut2 mRNA and fucosylation correlating with B. thetaiotaomicron growth. Inoculation of B. thetaiotaomicron in wild-type and NHE3−/− terminal ileum organoids displayed increased fut2 and fucosylation, indicating that B. thetaiotaomicron alone is sufficient for the increased fucosylation seen in vivo. These data demonstrate that loss of NHE3 alters the intestinal environment, leading to region-specific changes in bacteria, and shed light on the growth requirements of some gut microbiota members, which is vital for creating better treatments of complex diseases with an altered gut microbiota. PMID:24072680

  13. The Bfp60 surface adhesin is an extracellular matrix and plasminogen protein interacting in Bacteroides fragilis

    PubMed Central

    de Oliveira Ferreira, Eliane; Teixeira, Felipe; Cordeiro, Fabiana; Lobo, Leandro Araujo; Rocha, Edson R.; Smith, Jeffrey C.; Domingues, Regina M C P

    2014-01-01

    Plasminogen (Plg) is a highly abundant protein found in the plasma component of blood and is necessary for the degradation of fibrin, collagen, and other structural components of tissues. This fibrinolytic system is utilized by several pathogenic species of bacteria to manipulate the host plasminogen system and facilitate invasion of tissues during infection by modifying the activation of this process through the binding of Plg at their surface. Bacteroides fragilis is the most commonly isolated Gram-negative obligate anaerobe from human clinical infections, such as intra-abdominal abscesses and anaerobic bacteraemia. The ability of B. fragilis to convert plasminogen (Plg) into plasmin has been associated with an outer membrane protein named Bfp60. In this study, we characterized the function of Bfp60 protein in B. fragilis 638R by constructing the bfp60 defective strain and comparing its with that of the wild type regarding binding to laminin-1 (LMN-1) and activation of Plg into plasmin. Although the results showed in this study indicate that Bfp60 surface protein of B. fragilis is important for the recognition of LMN-1 and Plg activation, a significant slow activation of Plg into plasmin was observed in the mutant strain. For that reason, the possibility of another unidentified mechanism activating Plg is also present in B. fragilis can not be discarded. The results demonstrate that Bfp60 protein is responsible for the recognition of laminin and Plg-plasmin activation. Although the importance of this protein is still unclear in the pathogenicity of the species, it is accepted that since other pathogenic bacteria use this mechanism to disseminate through the extracellular matrix during the infection, it should also contribute to the virulence of B. fragilis. PMID:23850366

  14. Comparison of the transport of Bacteroides fragilis and Escherichia coli within saturated sand packs.

    PubMed

    Johanson, Jennifer J; Feriancikova, Lucia; Banerjee, Areen; Saffarini, Daâd A; Wang, Lixia; Li, Jin; Grundl, Timothy J; Xu, Shangping

    2014-11-01

    Pathogens in groundwater accounted for ∼50% of waterborne disease outbreaks in the United States between 1971 and 2006. The fast and reliable detection of groundwater microbial contamination and the identification of the contamination sources are of critical importance to the protection of public health. Recent studies suggested that fecal anaerobe Bacteriodes spp. could be employed as an effective tool for surface water microbial source tracking (MST). The usefulness of Bacteroides spp. for groundwater MST depends strongly on its mobility within the subsurface system. This research provides laboratory results comparing transport and attachment of E. coli K12 and B. fragilis within packed quartz sands. The results indicate that at low ionic strengths both E. coli K12 and B. fragilis are readily transported through saturated sand packs. At higher ionic strengths such as may be found near concentrated sources of fecal contamination, B. fragilis displayed significantly higher mobility than E. coli K12. Analysis of the extended Derjaguin-Landau-Verweu-Overbeek (XDLVO) energy interactions for both types of bacteria showed a significant repulsive energy barrier exists between the sand surface and the bacteria, precluding attachment directly to the sand surface. However a secondary minimum energy level exists under higher ionic strength conditions. The depth of this energy low is greater for E. coli K12, which results in greater attachment of E. coli K12 than of B. fragilis. The high mobility of B. fragilis suggests that it represents a promising tool for the detection of groundwater fecal contamination as well as the identification of the microbial sources. PMID:25448721

  15. The Bacteroides fragilis toxin fragilysin disrupts the paracellular barrier of epithelial cells.

    PubMed Central

    Obiso, R J; Azghani, A O; Wilkins, T D

    1997-01-01

    Bacteroides fragilis is a member of the normal colonic microflora of most mammals and is the most commonly isolated anaerobe from human clinical specimens. Some strains produce a toxin (fragilysin, a zinc-metalloproteinase) implicated as a cause of diarrheal disease in farm animals and humans. Studies in our laboratory confirm that the proteolytic activity of this toxin is responsible for the fluid secretion and tissue damage observed in vivo. In this study, we investigated the effects of fragilysin on the paracellular barrier of epithelial cells. Researchers suggest that, since the toxin rapidly intoxicates HT-29 cells, it may be internalized. However, we could not prevent cell rounding by using inhibitors of receptor-mediated endocytosis, which indicates that the toxin may act outside the cell. Based on these observations, we studied the effects of the highly purified B. fragilis fragilysin on the barrier function of cultured epithelial cells. Fragilysin rapidly increased the permeability of the paracellular barrier of epithelial cells to ions (decrease in electrical resistance across monolayers) and to larger molecules (increase in mannitol flux across monolayers). We tested a human colon cell line and cell lines from the lung and the kidney; the human colon cell line was most sensitive, but all three were affected in the same manner. Our studies show that B. fragilis fragilysin alters the barrier function of the epithelial lining, possibly by degrading the tight junction proteins, such as ZO-1. The proteolytic activity is required to cause this effect. The toxin's action has been assumed to be limited to the intestine; however, our studies show that fragilysin could also contribute to the pathogenesis of B. fragilis in extraintestinal infections. PMID:9119484

  16. Specific cell components of Bacteroides gingivalis mediate binding and degradation of human fibrinogen.

    PubMed Central

    Lantz, M S; Allen, R D; Vail, T A; Switalski, L M; Hook, M

    1991-01-01

    Bacteroides (Porphyromonas) gingivalis, which has been implicated as an etiologic agent in human periodontal diseases, has been shown to bind and degrade human fibrinogen. B. gingivalis strains bind fibrinogen reversibly and with high affinity and bind to a specific region of the fibrinogen molecule that appears to be located between the D and E domains (M. S. Lantz, R. D. Allen, P. Bounelis, L. M. Switalski, and M. Hook, J. Bacteriol. 172:716-726, 1990). We now report that human fibrinogen is bound and then degraded by specific B. gingivalis components that appear to be localized at the cell surface. Fibrinogen binding to bacterial cells occurred at 4, 22, and 37 degrees C. A functional fibrinogen-binding component (Mr, 150,000) was identified when sodium dodecyl sulfate-solubilized bacteria were fractionated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, transferred to nitrocellulose membranes, and probed with 125I-fibrinogen. Fibrinogen degradation did not occur at 4 degrees C but did occur at 22 and 37 degrees C. When bacteria and iodinated fibrinogen were incubated at 37 degrees C, two major fibrinogen fragments (Mr, 97,000 and 50,000) accumulated in incubation mixture supernatant fractions. Two major fibrinogen-degrading components (Mr, 120,000 and 150,000) have been identified by sodium dodecyl sulfate-polyacrylamide gel electrophoresis in substrate-containing gels. Fibrinogen degradation by the Mr-120,000 and -150,000 proteases was enhanced by reducing agents, completely inhibited by N-alpha-p-tosyl-L-lysyl chloromethyl ketone, and partially inhibited by n-ethyl maleimide, suggesting that these enzymes are thiol-dependent proteases with trypsinlike substrate specificity. The fibrinogen-binding component could be separated from the fibrinogen-degrading components by selective solubilization of bacteria in sodium deoxycholate. Images PMID:1987144

  17. Biochemical and genetic analyses of a catalase from the anaerobic bacterium Bacteroides fragilis.

    PubMed Central

    Rocha, E R; Smith, C J

    1995-01-01

    A single catalase enzyme was produced by the anaerobic bacterium Bacteroides fragilis when cultures at late log phase were shifted to aerobic conditions. In anaerobic conditions, catalase activity was detected in stationary-phase cultures, indicating that not only oxygen exposure but also starvation may affect the production of this antioxidant enzyme. The purified enzyme showed a peroxidatic activity when pyrogallol was used as an electron donor. It is a hemoprotein containing one heme molecule per holomer and has an estimated molecular weight of 124,000 to 130,000. The catalase gene was cloned by screening a B. fragilis library for complementation of catalase activity in an Escherichia coli catalase mutant (katE katG) strain. The cloned gene, designated katB, encoded a catalase enzyme with electrophoretic mobility identical to that of the purified protein from the B. fragilis parental strain. The nucleotide sequence of katB revealed a 1,461-bp open reading frame for a protein with 486 amino acids and a predicted molecular weight of 55,905. This result was very close to the 60,000 Da determined by denaturing sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the purified catalase and indicates that the native enzyme is composed of two identical subunits. The N-terminal amino acid sequence of the purified catalase obtained by Edman degradation confirmed that it is a product of katB. The amino acid sequence of KatB showed high similarity to Haemophilus influenzae HktE (71.6% identity, 66% nucleotide identity), as well as to gram-positive bacterial and mammalian catalases. No similarities to bacterial catalase-peroxidase-type enzymes were found. The active-site residues, proximal and distal hemebinding ligands, and NADPH-binding residues of the bovine liver catalase-type enzyme were highly conserved in B. fragilis KatB. PMID:7768808

  18. Molecular cloning and expression in Escherichia coli of a cellodextrinase gene from Bacteroides succinogenes S85.

    PubMed Central

    Gong, J H; Lo, R Y; Forsberg, C W

    1989-01-01

    A DNA fragment coding for a cellodextrinase of Bacteroides succinogenes S85 was isolated by screening of a pBR322 gene library in Escherichia coli HB101. Of 100,000 colonies screened on a complex medium with methylumbelliferyl-beta-D-cellobioside as the indicator substrate, two cellodextrinase-positive clones (CB1 and CB2) were isolated. The DNA inserts from the two recombinant plasmids were 7.7 kilobase pairs in size and had similar restriction maps. After subcloning from pCB2, a 2.5-kilobase-pair insert which coded for cellodextrinase activity was isolated. The enzyme was located in the cytoplasm of the E. coli host. It exhibited no activity on carboxymethyl cellulose, Avicel microcrystalline cellulose, acid-swollen cellulose, or cellobiose but hydrolyzed p-nitrophenyl-beta-D-cellobioside and p-nitrophenyl-beta-D-lactoside. The Km (0.1 mM) for the hydrolysis of p-nitrophenyl-cellobioside by the enzyme expressed in E. coli was similar to that reported for the purified enzyme from B. succinogenes. Expression of the cellodextrinase gene was subjected to catabolite repression by glucose and was not induced by cellobiose. The origin of the DNA insert from B. succinogenes was confirmed by Southern blot analysis. Western blotting (immunoblotting) using antibodies raised against the purified B. succinogenes cellodextrinase revealed a protein with a molecular weight of approximately 50,000 in E. coli clones which comigrated with the native enzyme isolated from B. succinogenes. These data indicate that the cellodextrinase gene expressed in E. coli is fully functional and codes for an enzyme with properties similar to those of the native enzyme. Images PMID:2650617

  19. Analysis of proteins associated with growth of Bacteroides ovatus on the branched galactomannan guar gum.

    PubMed Central

    Valentine, P J; Salyers, A A

    1992-01-01

    Bacteroides ovatus, a gram-negative obligate anaerobe from the human colon, can ferment the branched galactomannan guar gum. Previously, three enzymes involved in guar gum breakdown were characterized. The expression of these enzymes appeared to be regulated; i.e., specific activities were higher in extracts from bacteria grown on guar gum than in extracts from bacteria grown on the monosaccharide constituents of guar gum, mannose and galactose. In the present study, we used two-dimensional gel analysis to determine the total number of B. ovatus proteins enhanced during growth on guar gum. Twelve soluble proteins and 20 membrane proteins were expressed at higher levels in guar gum-grown cells than in galactose-grown cells. An unexpected finding was that the expression of the two galactomannanases was induced by glucose as well as guar gum. Three other proteins, one membrane protein and two soluble proteins, had this same expression pattern. The remainder of the guar gum-associated proteins seen on two-dimensional gels and the guar gum-associated alpha-galactosidase were induced in cells grown on guar gum but not in cells grown on glucose. Two transposon-generated mutants (M-5 and M-7) that could not grow on guar gum were isolated. Both mutants still expressed the galactomannanases and the alpha-galactosidase. They also still expressed all of the guar gum-associated proteins that could be detected in two-dimensional gels of glucose-grown or galactose-grown cells. A second transposon insertion that suppressed the guar gum-negative phenotype of M-5 was isolated and characterized. The characteristics of this suppressor mutant indicated that the original transposon insertion was probably in a regulatory locus. Images PMID:1622222

  20. Genetics and biochemistry of the Rhizobium meliloti acidic extracellular heteropolysaccharide and its role in nodulation: Annual report for the period 1 June 1987-31 May 1988

    SciTech Connect

    Leigh, J.A.

    1988-01-01

    The symbiotic association of Rhizobium with legumes results in a vital supply of inexpensive nitrogen for the growth of crops such as soybean and alfalfa. In a complex series of events, the bacterial symbiont, Rhizobium, induces the formation of a specialilzed root structure, the nodule. Rhizobium then enters the cells of the nodule and fixes nitrogen. We are interested in an extracellular polysaccharide, produced by Rhizobium, which is required for nodule entry. We have found that R. meliloti mutants which produce the polysaccharide but fail to enter nodules, actually produce an abnormal form of the polysacchardie which lacks succinate. Recently we have discovered a second polysaccharide which can be produced in place of the first polysacchaaride and also satisfy the requirement for nodule entry. We are studying the gentic regulation of the production of the two polysaccharides.

  1. Mechanism of acid tolerance in a rhizobium strain isolated from Pueraria lobata (Willd.) Ohwi.

    PubMed

    Lei, Zhang; Jian-ping, Gu; Shi-qing, Wei; Ze-yang, Zhou; Chao, Zhang; Yongxiong, Yu

    2011-06-01

    The Rhizobium sp. strain PR389 was isolated from the root nodules of Pueraria lobata (Willd.) Ohwi, which grows in acidic (pH 4.6) yellow soil of the Jinyun Mountains of Beibei, Chongqing, China. While rhizobia generally have a pH range of 6.5-7.5 for optimum growth, strain PR389 grew in a liquid yeast extract - mannitol agar medium at pH 4.6, as well as in a pH 4.1 soil suspension, suggesting acid tolerance in this specific strain of rhizobium . However, at pH 4.6, the lag phase before vigorous growth was 40 h compared with 4 h under neutral conditions (pH 7.0). For PR389, the generation time after the lag phase remained the same at different pH levels despite the different durations of the lag phase. Except in the pH 4.4 treatment, the pH of the culturing media increased from 4.6, 4.8, 5.0, and 5.5 to neutral and slightly alkaline after 70 h of culture. Chloramphenicol was added to determine if protein production was involved in the increasing pH process. Chloramphenicol significantly inhibited PR389 growth under acid stress but had little effect under neutral conditions. Proton flux measured during a short acid shock (pH 3.8) revealed that this strain has an intrinsic ability to prevent H(+) from entering cells when compared with acid-sensitive rhizobia. We propose that the mechanism for acid tolerance in PR389 involves both intracellular and extracellular processes. When the extracellular pH is lower than pH 4.4, the cell membrane blocks hydrogen from entering the cell. When the pH exceeds 4.4, the rhizobium strain has the ability to raise the extracellular pH, thereby, potentially decreasing the toxicity of aluminum in acid soil. PMID:21635219

  2. Changes in the Common Bean Transcriptome in Response to Secreted and Surface Signal Molecules of Rhizobium etli1[OPEN

    PubMed Central

    Dalla Via, Virginia; Narduzzi, Candela; Aguilar, Orlando Mario; Zanetti, María Eugenia; Blanco, Flavio Antonio

    2015-01-01

    Establishment of nitrogen-fixing symbiosis requires the recognition of rhizobial molecules to initiate the development of nodules. Using transcriptional profiling of roots inoculated with mutant strains defective in the synthesis of Nod Factor (NF), exopolysaccharide (EPS), or lipopolysaccharide (LPS), we identified 2,606 genes from common bean (Phaseolus vulgaris) that are differentially regulated at early stages of its interaction with Rhizobium etli. Many transcription factors from different families are modulated by NF, EPS, and LPS in different combinations, suggesting that the plant response depends on the integration of multiple signals. Some receptors identified as differentially expressed constitute excellent candidates to participate in signal perception of molecules derived from the bacteria. Several components of the ethylene signal response, a hormone that plays a negative role during early stages of the process, were down-regulated by NF and LPS. In addition, genes encoding proteins involved in small RNA-mediated gene regulation were regulated by these signal molecules, such as Argonaute7, a specific component of the trans-acting short interfering RNA3 pathway, an RNA-dependent RNA polymerase, and an XH/XP domain-containing protein, which is part of the RNA-directed DNA methylation. Interestingly, a number of genes encoding components of the circadian central oscillator were down-regulated by NF and LPS, suggesting that a root circadian clock is adjusted at early stages of symbiosis. Our results reveal a complex interaction of the responses triggered by NF, LPS, and EPS that integrates information of the signals present in the surface or secreted by rhizobia. PMID:26282238

  3. Genetic basis for Rhizobium etli CE3 O-antigen O-methylated residues that vary according to growth conditions.

    PubMed

    Ojeda, Kristylea J; Box, Jodie M; Noel, K Dale

    2010-02-01

    The Rhizobium etli CE3 O antigen is a fixed-length heteropolymer with O methylation being the predominant type of sugar modification. There are two O-methylated residues that occur, on average, once per complete O antigen: a multiply O-methylated terminal fucose and 2-O methylation of a fucose residue within a repeating unit. The amount of the methylated terminal fucose decreases and the amount of 2-O-methylfucose increases when bacteria are grown in the presence of the host plant, Phaseolus vulgaris, or its seed exudates. Insertion mutagenesis was used to identify open reading frames required for the presence of these O-methylated residues. The presence of the methylated terminal fucose required genes wreA, wreB, wreC, wreD, and wreF, whereas 2-O methylation of internal fucoses required the methyltransferase domain of bifunctional gene wreM. Mutants lacking only the methylated terminal fucose, lacking only 2-O methylation, or lacking both the methylated terminal fucose and 2-O methylation exhibited no other lipopolysaccharide structural defects. Thus, neither of these decorations is required for normal O-antigen length, transport, or assembly into the final lipopolysaccharide. This is in contrast to certain enteric bacteria in which the absence of a terminal decoration severely affects O-antigen length and transport. R. etli mutants lacking only the methylated terminal fucose were not altered in symbiosis with host Phaseolus vulgaris, whereas mutants lacking only 2-O-methylfucose exhibited a delay in nodule development during symbiosis. These results support previous conclusions that the methylated terminal fucose is dispensable for symbiosis, whereas 2-O methylation of internal fucoses somehow facilitates early events in symbiosis. PMID:19948805

  4. Genetic Basis for Rhizobium etli CE3 O-Antigen O-Methylated Residues That Vary According to Growth Conditions▿

    PubMed Central

    Ojeda, Kristylea J.; Box, Jodie M.; Noel, K. Dale

    2010-01-01

    The Rhizobium etli CE3 O antigen is a fixed-length heteropolymer with O methylation being the predominant type of sugar modification. There are two O-methylated residues that occur, on average, once per complete O antigen: a multiply O-methylated terminal fucose and 2-O methylation of a fucose residue within a repeating unit. The amount of the methylated terminal fucose decreases and the amount of 2-O-methylfucose increases when bacteria are grown in the presence of the host plant, Phaseolus vulgaris, or its seed exudates. Insertion mutagenesis was used to identify open reading frames required for the presence of these O-methylated residues. The presence of the methylated terminal fucose required genes wreA, wreB, wreC, wreD, and wreF, whereas 2-O methylation of internal fucoses required the methyltransferase domain of bifunctional gene wreM. Mutants lacking only the methylated terminal fucose, lacking only 2-O methylation, or lacking both the methylated terminal fucose and 2-O methylation exhibited no other lipopolysaccharide structural defects. Thus, neither of these decorations is required for normal O-antigen length, transport, or assembly into the final lipopolysaccharide. This is in contrast to certain enteric bacteria in which the absence of a terminal decoration severely affects O-antigen length and transport. R. etli mutants lacking only the methylated terminal fucose were not altered in symbiosis with host Phaseolus vulgaris, whereas mutants lacking only 2-O-methylfucose exhibited a delay in nodule development during symbiosis. These results support previous conclusions that the methylated terminal fucose is dispensable for symbiosis, whereas 2-O methylation of internal fucoses somehow facilitates early events in symbiosis. PMID:19948805

  5. Varying the Abundance of O Antigen in Rhizobium etli and Its Effect on Symbiosis with Phaseolus vulgaris

    PubMed Central

    Noel, K. Dale; Forsberg, Lennart S.; Carlson, Russell W.

    2000-01-01

    Judged by migration of its lipopolysaccharide (LPS) in gel electrophoresis, the O antigen of Rhizobium etli mutant strain CE166 was apparently of normal size. However, its LPS sugar composition and staining of the LPS bands after electrophoresis indicated that the proportion of its LPS molecules that possessed O antigen was only 40% of the wild-type value. Its LPS also differed from the wild type by lacking quinovosamine (2-amino-2,6-dideoxyglucose). Both of these defects were due to a single genetic locus carrying a Tn5 insertion. The deficiency in O-antigen amount, but not the absence of quinovosamine, was suppressed by transferring into this strain recombinant plasmids that shared a 7.8-kb stretch of the R. etli CE3 lps genetic region α, even though this suppressing DNA did not carry the genetic region mutated in strain CE166. Strain CE166 gave rise to pseudonodules on legume host Phaseolus vulgaris, whereas the mutant suppressed by DNA from lps region α elicited nitrogen-fixing nodules. However, the nodules in the latter case developed slowly and were widely dispersed. Two other R. etli mutants that had one-half or less of the normal amount of O antigen also gave rise to pseudonodules on P. vulgaris. The latter strains were mutated in lps region α and could be restored to normal LPS content and normal symbiosis by complementation with wild-type DNA from this region. Hence, the symbiotic role of LPS requires near-normal abundance of O antigen and may require a structural feature conferred by quinovosamine. PMID:10986232

  6. The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function

    PubMed Central

    Das, Debanu; Finn, Robert D.; Carlton, Dennis; Miller, Mitchell D.; Abdubek, Polat; Astakhova, Tamara; Axelrod, Herbert L.; Bakolitsa, Constantina; Chen, Connie; Chiu, Hsiu-Ju; Chiu, Michelle; Clayton, Thomas; Deller, Marc C.; Duan, Lian; Ellrott, Kyle; Ernst, Dustin; Farr, Carol L.; Feuerhelm, Julie; Grant, Joanna C.; Grzechnik, Anna; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K.; Klock, Heath E.; Knuth, Mark W.; Kozbial, Piotr; Krishna, S. Sri; Kumar, Abhinav; Marciano, David; McMullan, Daniel; Morse, Andrew T.; Nigoghossian, Edward; Nopakun, Amanda; Okach, Linda; Puckett, Christina; Reyes, Ron; Rife, Christopher L.; Sefcovic, Natasha; Tien, Henry J.; Trame, Christine B.; van den Bedem, Henry; Weekes, Dana; Wooten, Tiffany; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Elsliger, Marc-André; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A.

    2010-01-01

    Proteins that contain the DUF2874 domain constitute a new Pfam family PF11396. Members of this family have predominantly been identified in microbes found in the human gut and oral cavity. The crystal structure of one member of this family, BVU2987 from Bacteroides vulgatus, has been determined, revealing a β-lactamase inhibitor protein-like structure with a tandem repeat of domains. Sequence analysis and structural comparisons reveal that BVU2987 and other DUF2874 proteins are related to β-lactamase inhibitor protein, PepSY and SmpA_OmlA proteins and hence are likely to function as inhibitory proteins. PMID:20944221

  7. Competitive PCR for quantitation of a Cytophaga-Flexibacter-Bacteroides phylum bacterium associated with the Tuber borchii Vittad. mycelium.

    PubMed

    Barbieri, Elena; Riccioni, Giulia; Pisano, Anna; Sisti, Davide; Zeppa, Sabrina; Agostini, Deborah; Stocchi, Vilberto

    2002-12-01

    An uncultured bacterium associated with the ectomycorrhizal fungus Tuber borchii Vittad. was identified as a novel member of the Cytophaga-Flexibacter-Bacteroides group. Utilizing a quantitative PCR targeting the 16S rRNA gene, we relatively quantified this bacterium in the host. The estimated number of bacteria was found to be approximately 10(6) cells per 30-day-old T. borchii mycelium culture. This represents the first molecular attempt to enumerate an uncultured bacterium associated with a mycorrhizal fungus. PMID:12450871

  8. Effectiveness of halo-tolerant, auxin producing Pseudomonas and Rhizobium strains to improve osmotic stress tolerance in mung bean (Vigna radiata L.)

    PubMed Central

    Ahmad, Maqshoof; Zahir, Zahir A.; Nazli, Farheen; Akram, Fareeha; Arshad, Muhammad; Khalid, Muhammad

    2013-01-01

    Halo-tolerant, auxin producing bacteria could be used to induce salt tolerance in plants. A number of Rhizobium and auxin producing rhizobacterial strains were assessed for their ability to tolerate salt stress by conducting osmoadaptation assay. The selected strains were further screened for their ability to induce osmotic stress tolerance in mung bean seedlings under salt-stressed axenic conditions in growth pouch/jar trials. Three most effective strains of Rhizobium and Pseudomonas containing ACC-deaminase were evaluated in combination, for their ability to induce osmotic stress tolerance in mung bean at original, 4, and 6 dS m−1 under axenic conditions. Results showed that sole inoculation of Rhizobium and Pseudomonas strains improved the total dry matter up to 1.4, and 1.9 fold, respectively, while the increase in salt tolerance index was improved up to 1.3 and 2.0 fold by the Rhizobium and Pseudomonas strains, respectively. However, up to 2.2 fold increase in total dry matter and salt tolerance index was observed due to combined inoculation of Rhizobium and Pseudomonas strains. So, combined application of Rhizobium and Pseudomonas strains could be explored as an effective strategy to induce osmotic stress tolerance in mung bean. PMID:24688532

  9. Vitamin B12 Uptake by the Gut Commensal Bacteria Bacteroides thetaiotaomicron Limits the Production of Shiga Toxin by Enterohemorrhagic Escherichia coli

    PubMed Central

    Cordonnier, Charlotte; Le Bihan, Guillaume; Emond-Rheault, Jean-Guillaume; Garrivier, Annie; Harel, Josée; Jubelin, Grégory

    2016-01-01

    Enterohemorrhagic Escherichia coli (EHEC) are foodborne pathogens responsible for the development of bloody diarrhea and renal failure in humans. Many environmental factors have been shown to regulate the production of Shiga toxin 2 (Stx2), the main virulence factor of EHEC. Among them, soluble factors produced by human gut microbiota and in particular, by the predominant species Bacteroides thetaiotaomicron (B. thetaiotaomicron), inhibit Stx2 gene expression. In this study, we investigated the molecular mechanisms underlying the B. thetaiotaomicron-dependent inhibition of Stx2 production by EHEC. We determined that Stx2-regulating molecules are resistant to heat treatment but do not correspond to propionate and acetate, two short-chain fatty acids produced by B. thetaiotaomicron. Moreover, screening of a B. thetaiotaomicron mutant library identified seven mutants that do not inhibit Stx2 synthesis by EHEC. One mutant has impaired production of BtuB, an outer membrane receptor for vitamin B12. Together with restoration of Stx2 level after vitamin B12 supplementation, these data highlight vitamin B12 as a molecule produced by gut microbiota that modulates production of a key virulence factor of EHEC and consequently may affect the outcome of an infection. PMID:26742075

  10. [Characteristics of Natural Selection in Populations of Nodule Bacteria (Rhizobium leguminosarum) Interacting With Different Host Plants].

    PubMed

    Andronov, E E; Igolkina, A A; Kimeklis, A K; Vorobyov, N I; Provorov, N A

    2015-10-01

    Using high throughput sequencing of the nodA gene, we studied the population dynamics of Rhizobium leguminosarum (bv. viciae, bv. trifolii) in rhizospheric and nodular subpopulations associated with the leguminous plants representing different cross-inoculation groups (Vicia sativa, Lathyrus pratensis of the vetch/vetchling/pea group and Trifolium hybridum of the clover group). The "rhizosphere-nodules" transitions result in either an increase or decrease in the frequencies of 10 of the 23 operational taxonomic units (OTUs) (which were identified with 95% similarity) depending on the symbiotic specificity and phylogenetic positions of OTUs. Statistical and bioinformatical analysis of the population structures suggest that the type of natural selection responsible for these changes may be diversifying at the whole-population level and frequency-dependent at the OTU-specific level, ensuring the divergent evolution of rhizobia interacting with different host species. PMID:27169225

  11. Synergy between Rhizobium phaseoli and Acidithiobacillus ferrooxidans in the Bioleaching Process of Copper.

    PubMed

    Zheng, Xuecheng; Li, Dongwei

    2016-01-01

    This study investigates the synergy of Rhizobium phaseoli and Acidithiobacillus ferrooxidans in the bioleaching process of copper. The results showed that additional R. phaseoli could increase leaching rate and cell number of A. ferrooxidans. When the initial cell number ratio between A. ferrooxidans and R. phaseoli was 2 : 1, A. ferrooxidans attained the highest final cell number of approximately 2 × 10(8) cells/mL and the highest copper leaching rate of 29%, which is 7% higher than that in the group with A. ferrooxidans only. R. phaseoli may use metabolized polysaccharides from A. ferrooxidans, and organic acids could chelate or precipitate harmful heavy metals to reduce their damage on A. ferrooxidans and promote its growth. Organic acids could also damage the mineral lattice to increase the leaching effect. PMID:26942203

  12. Environmental Factors Influencing Numbers of Rhizobium leguminosarum biovar trifolii and Its Bacteriophages in Two Field Soils.

    PubMed

    Lawson, K A; Barnet, Y M; McGilchrist, C A

    1987-05-01

    Fluctuations in numbers of Rhizobium leguminosarum biovar trifolii and its bacteriophages in two fields with different soil types were followed during a 17-month period in 1981 and 1982. Mean levels of both phage and rhizobia varied significantly (P < 0.05) on different occasions, with rhizobial levels varying from 1.6 x 10 to 2.0 x 10 cell per g of soil and phage from 0 to 1.7 x 10 PFU/g of soil. Multivariate regression analysis showed rhizobial levels to be significantly and positively related to vegetation height and solar radiation, but not to mean temperature, precipitation, soil matric potential, or soil type. Rhizobiophage concentrations were significantly and positively related to soil matric potential and vegetation height. They were reduced in the silty clay loam soil, although the presence of 34% clay did not prevent phage multiplication and the occurrence of high phage levels. PMID:16347339

  13. Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain TA1

    PubMed Central

    Reeve, Wayne; Tian, Rui; De Meyer, Sofie; Melino, Vanessa; Terpolilli, Jason; Ardley, Julie; Tiwari, Ravi; Howieson, John; Yates, Ronald; O’Hara, Graham; Ninawi, Mohamed; Teshima, Hazuki; Bruce, David; Detter, Chris; Tapia, Roxanne; Han, Cliff; Wei, Chia-Lin; Huntemann, Marcel; Han, James; Chen, I-Min; Mavromatis, Konstantinos; Markowitz, Victor; Ivanova, Natalia; Ovchinnikova, Galina; Pagani, Ioanna; Pati, Amrita; Goodwin, Lynne; Pitluck, Sam; Woyke, Tanja; Kyrpides, Nikos

    2013-01-01

    Rhizobium leguminosarum bv. trifolii strain TA1 is an aerobic, motile, Gram-negative, non-spore-forming rod that is an effective nitrogen fixing microsymbiont on the perennial clovers originating from Europe and the Mediterranean basin. TA1 however is ineffective with many annual and perennial clovers originating from Africa and America. Here we describe the features of R. leguminosarum bv. trifolii strain TA1, together with genome sequence information and annotation. The 8,618,824 bp high-quality-draft genome is arranged in a 6 scaffold of 32 contigs, contains 8,493 protein-coding genes and 83 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program. PMID:24976881

  14. Environmental Factors Influencing Numbers of Rhizobium leguminosarum biovar trifolii and Its Bacteriophages in Two Field Soils

    PubMed Central

    Lawson, Kerrie A.; Barnet, Yvonne M.; McGilchrist, Clyde A.

    1987-01-01

    Fluctuations in numbers of Rhizobium leguminosarum biovar trifolii and its bacteriophages in two fields with different soil types were followed during a 17-month period in 1981 and 1982. Mean levels of both phage and rhizobia varied significantly (P < 0.05) on different occasions, with rhizobial levels varying from 1.6 × 102 to 2.0 × 104 cell per g of soil and phage from 0 to 1.7 × 104 PFU/g of soil. Multivariate regression analysis showed rhizobial levels to be significantly and positively related to vegetation height and solar radiation, but not to mean temperature, precipitation, soil matric potential, or soil type. Rhizobiophage concentrations were significantly and positively related to soil matric potential and vegetation height. They were reduced in the silty clay loam soil, although the presence of 34% clay did not prevent phage multiplication and the occurrence of high phage levels. PMID:16347339

  15. Synergy between Rhizobium phaseoli and Acidithiobacillus ferrooxidans in the Bioleaching Process of Copper

    PubMed Central

    Zheng, Xuecheng; Li, Dongwei

    2016-01-01

    This study investigates the synergy of Rhizobium phaseoli and Acidithiobacillus ferrooxidans in the bioleaching process of copper. The results showed that additional R. phaseoli could increase leaching rate and cell number of A. ferrooxidans. When the initial cell number ratio between A. ferrooxidans and R. phaseoli was 2 : 1, A. ferrooxidans attained the highest final cell number of approximately 2 × 108 cells/mL and the highest copper leaching rate of 29%, which is 7% higher than that in the group with A. ferrooxidans only. R. phaseoli may use metabolized polysaccharides from A. ferrooxidans, and organic acids could chelate or precipitate harmful heavy metals to reduce their damage on A. ferrooxidans and promote its growth. Organic acids could also damage the mineral lattice to increase the leaching effect. PMID:26942203

  16. Comparison of the activity of imipenem and beta-lactams combined with sulbactam and clavulanic acid in beta-lactamase-producing strains of Bacteroides fragilis.

    PubMed

    Martín, M A; Castillo, A M; Liébana, J; Marín, A; Alados, J C; Piédrola, G

    1991-01-01

    We compared the "in vitro" activity of imipenem with 14 beta-lactams, both alone and in combination with clavulanic acid, and sulbactam against 110 beta-lactamase-producing strains of Bacteroides fragilis. The following antibiotics were tested: amoxycillin, penicillin, mezlocillin, piperacillin, cephalothin, cephazolin, cefamandole, cefmetazole, cefonicid, cefoxitin, cefotaxime, ceftazidime, ceftizoxime, and ceftriaxone. In all cases, except those of cefoxitin and cefmetazole, these combinations showed a statistically significant increase in beta-lactam activity, which was, however, never higher than that of imipenem, the antibiotic which performed best against Bacteroides fragilis. PMID:1940333

  17. Field study of a soil-soybean plant-Rhizobium system amended with cadmium

    SciTech Connect

    Borges, A.C.; Wollum, A.G. II

    1980-07-01

    Soybean plants (Glycine max (L.) Merr.) were cropped over a period of 3 years, under field conditions, in a soil amended with Cd (as CdCl/sub 2/ . 2 1/2 H/sub 2/O) at rates corresponding to 0, 3.3, 12.5, and 22.8 kg Cd/ha in order to evaluate the effect of Cd on seed yield, Cd accumulation in seeds, and the distribution of indigenous Rhizobium japonicum strains. Cadmium migration from the cultivated layers of the subsoil during 3 years was not significant. Soybean seed yields were affected significantly only when DTPA-TEA-extractable Cd was > 1.57 ..mu..g Cd/g in the cultivated layers of the soil, suggesting that only in cases of extreme Cd contamination would significant yield reduction occur. Cadmium content of seeds increased from year to year with values > 1 ..mu..g Cd/g being found only when Cd had been added. Grain yield decreased only in the high Cd treatments. Therefore, grain yield would be a poor indicator of Cd contamination in a soil cropped with soybeans. The results also suggested DTPA-TEA-extractable soil Cd does not accurately measure the readily available pool of Cd for soybean plants. Rather Cd content of seeds appears to be a better indicator of the extent of Cd contamination. Rhizobium japonicum strain distribution was not affected by the presence of Cd in the soil. Sero-groups 24, 31, 76, and 94 dominated the area surveyed.

  18. Cell-associated pectinolytic and cellulolytic enzymes in Rhizobium leguminosarum biovar trifolii.

    PubMed Central

    Mateos, P F; Jimenez-Zurdo, J I; Chen, J; Squartini, A S; Haack, S K; Martinez-Molina, E; Hubbell, D H; Dazzo, F B

    1992-01-01

    The involvement of Rhizobium enzymes that degrade plant cell wall polymers has long been an unresolved question about the infection process in root nodule symbiosis. Here we report the production of enzymes from Rhizobium leguminosarum bv. trifolii that degrade carboxymethyl cellulose and polypectate model substrates with sensitive methods that reliably detect the enzyme activities: a double-layer plate assay, quantitation of reducing sugars with a bicinchoninate reagent, and activity gel electrophoresis-isoelectric focusing. Both enzyme activities were (i) produced commonly by diverse wild-type strains, (ii) cell bound with at least some of the activity associated with the cell envelope, and (iii) not changed appreciably by growth in the presence of the model substrates or a flavone that activates expression of nodulation (nod) genes on the resident symbiotic plasmid (pSym). Equivalent levels of carboxymethyl cellulase activity were found in wild-type strain ANU843 and its pSym-cured derivative, ANU845, consistent with previous results of Morales et al. (V. Morales, E. Martínez-Molina, and D. Hubbell, Plant Soil 80:407-415, 1984). However, polygalacturonase activity was lower in ANU845 and was not restored to wild-type levels in the recombinant derivative of pSym- ANU845 containing the common and host-specific nod genes within a 14-kb HindIII DNA fragment of pSym from ANU843 cloned on plasmid pRt032. Activity gel electrophoresis resolved three carboxymethyl cellulase isozymes of approximately 102, 56, and 33 kDa in cell extracts from ANU843. Isoelectric focusing activity gels revealed one ANU843 polygalacturonase isozyme with a pI of approximately 7.2. These studies show that R. leguminosarum bv. trifolii produces multiple enzymes that cleave glycosidic bonds in plant cell walls and that are cell bound. Images PMID:1622257

  19. NAD- and NADP-dependent 7alpha-hydroxysteroid dehydrogenases from bacteroides fragilis.

    PubMed

    Macdonald, I A; Williams, C N; Mahony, D E; Christie, W M

    1975-03-28

    Twenty strains of Bacteroides fragilis were screened for hydroxysteroid oxidoreductase activity in cell-free preparations. Eighteen strains were shown to contain NAD-dependent 7alpha-hydroxysteroid dehydrogenase. Sixteen of the strains containing the NAD-dependent enzyme also contained NADP-depedent 7alpha-hydroxysteroid dehydrogenase, but invariably in lesser amounts. A strain particulary rich in both 7alpha-hydroxysteroid dehydrogenase activities was selected for further study. Measurement of activity as a function of pH revealed a fairly sharp optimal activity range of 9.5--10.0 for the NAD-dependent enzyme and a broad flat optimal range of 7.0--9.0 for the NADP-dependent enzyme. Michaelis constants for trihydroxy-bile acids for the NAD-dependent enzyme were in the range of 0.32--0.34 mM, whereas dihydroxy-bile acids gave a Km of 0.1 mM. Thin-layer chromatography studies on the oxidation product of 3alpha, 7alpha-dihydroxy-5beta-cholanoic acid (chenodeoxycholic acid) by the dehydrogenase revealed a band corresponding to that of synthetic 3alpha-hydroxy, 7-keto-5beta-cholanoic acid. Similarly the oxidation product of chenodeoxycholic acid by both 7alpha-hydroxysteroid dehydrogenase and commercially available 3alpha-hy-droxysteroid dehydrogenase revealed a band corresponding to that of synthetic 3,7-diketo-5beta-cholanoic acid. Neither of these two oxidation products could be distinguished from those by the Escherichia coli dehydrogenase oxidation previously reported. Disc-gel electrophoresis of a cell-free lyophilized preparation indicated one active band for NAD-dependent activity of mobility similar to that for the NADP-dependent E. coli enzyme. The NADP-dependent dehydrogenase was unstable and rapidly lost activity after polyacylamide disc-gel electrophoresis, ultracentrifugation, freezing on refrigeration at 4 degrees C. No 3 alpha- or 12alpha-oriented oxidoreductase activity was demonstrated in any of the strains examined. PMID:236764

  20. Restriction endonuclease analysis and ribotyping differentiate genital and nongenital strains of Bacteroides ureolyticus.

    PubMed Central

    Akhtar, N; Eley, A

    1992-01-01

    Thirty-three clinical isolates from male nongonococcal urethritis and 28 isolates from soft tissue infections and ulcers were identified as Bacteroides ureolyticus by conventional bacteriological tests and were compared with five reference strains of the species. Whole-cell proteins from these clinical isolates and the reference strains were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The majority of the strains from the two sources could be divided into five different groups, named phenons I to V; phenons I to IV have been described previously by others, while phenon V has been described recently by us. Digestion of chromosomal DNA from 16 of the clinical isolates (including strains representative of each of the five SDS-PAGE phenons) and the five reference strains was attempted with restriction endonucleases EcoRI, PstI, SmaI, and HindIII. After electrophoresis in agarose gels, good digestion was observed with HindIII only, and 12 different banding patterns (restriction endonuclease analysis [REA] profiles) were obtained for the 19 strains digested; one nongonococcal urethritis isolate and one reference strain did not show any digestion. From the agarose gels, HindIII-digested fragments of DNA were transferred to nylon membranes by use of vacuum blotting and subjected to hybridization with 32P-labelled 16S-23S rRNA from Escherichia coli. The resultant pattern of bands (ribotypes), which depends on the restriction fragment length polymorphisms in the rRNA genes, was used as a measure of genomic variation within the species. In total, 13 different ribotypes were obtained for the 19 strains. For some strains, good correlation was achieved among the SDS-PAGE phenons, REA profiles, and ribotypes. However, for others, REA analysis and ribotyping were able to discriminate between strains which shared the same SDS-PAGE phenon. Interestingly, these two techniques of DNA characterization were able to differentiate between isolates

  1. Porphyromonas (Bacteroides) gingivalis fimbrillin: size, amino-terminal sequence, and antigenic heterogeneity.

    PubMed Central

    Lee, J Y; Sojar, H T; Bedi, G S; Genco, R J

    1991-01-01

    Bacterial fimbriae mediate cell adhesion and are important in colonization. Fimbrial proteins from strains of Porphyromonas (Bacteroides) gingivalis isolated from different individuals were compared for their size, amino-terminal sequence, and antigenic diversity. Two major protein components of the crude fimbrial preparations differed in apparent molecular mass, ranging from 41 to 49 kDa for the fimbrillin monomer and from 61 to 78 kDa for the other major protein. The amino-terminal sequence of the antigenically related group of proteins of the fimbrillin monomer in the 41- to 49-kDa range showed significant homology; however, minor sequence heterogeneity was observed, mainly in residues 4 to 6. One of the observed amino-terminal sequences, AFGVGDDESKVAKLTVMVYNG, resembled the deduced sequence of P. gingivalis 381 (D.P. Dickinson, M. K. Kubiniec, F. Yoshimura, and R.J. Genco, J. Bacteriol. 170:1658-1665, 1988). Fimbriae from all the strains of P. gingivalis showing this sequence contained a fimbrillin monomer of 43 kDa and showed a strong reaction with both polyclonal and monoclonal antibodies directed to the fimbriae from P. gingivalis 2561 (381). Fimbriae from strains showing amino-terminal sequence variations in residues 4 to 6 (i.e., substitution of VGD with either E or NAG) were more diverse in their molecular sizes. Most of these variant fimbriae showed weak reactions with the polyclonal antibodies and no reaction with the monoclonal antibodies induced to the fimbriae of strain 2561. No correlation could be established between the molecular size and immunological reactivity of the fimbrillin monomer of P. gingivalis strains. Strains 9-14K-1 and HG 564 not only showed markedly different sequences from the other three amino-terminal sequences but also did not react with either polyclonal or monoclonal antibodies to the fimbriae of strain 2561. Strains W50, W83, and AJW 5 failed to show any immunological reactivity with the antibodies to fimbrillin or fimbriae

  2. Pharmacodynamics of Trovafloxacin and Levofloxacin against Bacteroides fragilis in an In Vitro Pharmacodynamic Model

    PubMed Central

    Peterson, M. L.; Hovde, L. B.; Wright, D. H.; Brown, G. H.; Hoang, A. D.; Rotschafer, J. C.

    2002-01-01

    An in vitro pharmacodynamic investigation was conducted to explore whether the area under the concentration time curve from 0 to 24 h (AUC0–24)/MIC ratio could predict fluoroquinolone performance against Bacteroides fragilis. An in vitro model was used to generate kill curves for trovafloxacin (TVA) and levofloxacin (LVX) at AUC0–24/MIC ratios of 1 to 406 against three strains of B. fragilis (ATCC 25285, ATCC 23745, and clinical isolate M97-117). TVA and LVX were bolused prior to the start of experiments to achieve the corresponding AUC0–24/MIC ratio. Experiments were performed in duplicate over 24 h and in an anaerobic environment. Analyses of antimicrobial performance were conducted by comparing the rates of bacterial kill (K) using nonlinear regression analysis with 95% confidence intervals. Statistical significance was defined as a lack of overlap in the 95% confidence limits generated from the slope of each kill curve. For both TVA and LVX, K was maximized once an AUC0–24/MIC ratio of ≥40 was achieved and was not further increased despite a 10-fold increase in AUC0–24/MIC from approximately 40 to 400 against all three strains of B. fragilis. No significant differences were found in K between AUC0–24/MIC ratios of approximately 40 to 200. In experiments where AUC0–24/MIC ratios that were ≥ 5 and ≤ 44 were conducted, 64% demonstrated regrowth at 24 h. Resistant strains were selected in 50% of those experiments, demonstrating regrowth, which resulted in increased MICs of two- to 16-fold for both TVA and LVX. Regrowth did not occur, nor were resistant strains selected in any studies with an AUC/MIC that was > 44. Our findings suggest that fluoroquinolones provide antibacterial effects against B. fragilis in a concentration-independent manner associated with an AUC0–24/MIC ratio of ≥40. Also, the potential for the selection of resistant strains of B. fragilis may increase with an AUC0–24/MIC ratio of ≤44. PMID:11751135

  3. Variation in the structural subunit and basal protein antigens of Bacteroides nodosus fimbriae.

    PubMed Central

    Anderson, B J; Kristo, C L; Egerton, J R; Mattick, J S

    1986-01-01

    The fimbriae of Bacteroides nodosus play a major role in protective immunity against ovine footrot and are an important determinant in the serological classification system that divides field isolates into at least eight serogroups and 16 serotypes. Purified fimbriae contain two polypeptide antigens, the structural subunit of the fimbrial strand (molecular weight about 17,000) and a basal protein (molecular weight about 80,000), both of which exhibit structural variation. Fimbriae were prepared from all prototype strains, as well as from a number of other isolates representative of each of the B. nodosus serotypes, and analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Substantial variation was observed in the electrophoretic mobility of the fimbrial subunits from the prototypes of each of the eight serogroups. With the exception of serogroup H, which is an unusual case, the apparent molecular weights of the fimbrial subunits ranged from about 16,500 in serogroup D to 19,000 in serogroup F (serotype 1); in serogroup A, B, C and E, the apparent molecular weights were clustered in the range of 17,000 to 17,500, whereas serogroup G was about 18,500. Serogroup H fimbriae appeared to consist of two smaller polypeptides, which in the prototype (H1) had apparent molecular weights of about 6,000 and 10,000 and which seem to have arisen as a consequence of an internal proteolytic nick in the original subunit. Electrophoretic variation in the fimbrial subunit was also observed between different serotypes, although with the exceptions of serogroups F and H, this was not as pronounced as between the serogroups. Examination of a number of isolates classified within the same serotypes showed that some variation, although minor, also occurred at this level. The basal antigen exhibited significant variation at all levels of the serotypic hierarchy in a manner apparently unrelated to the classification system. Among the range of isolates examined, the apparent

  4. The survival rate of Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, and Bacteroides forsythus following 4 randomized treatment modalities.

    PubMed

    Shiloah, J; Patters, M R; Dean, J W; Bland, P; Toledo, G

    1997-08-01

    The overall goal of this clinical study was to determine the short-term anti-infective effects of four randomized treatment modalities on Actinobacillus actinomycetemcomitans (Aa), Porphyromonas gingivalis (Pg), and Bacteroides forsythus (Bf) and determine the effects of bacterial survival on treatment outcomes in patients with adult periodontitis. Twelve adult patients requiring therapy for moderate periodontitis were selected for this study. All patients had at least one tooth in each quadrant that had an inflamed pocket of probing depth > or =5 mm with probing attachment loss that harbored at least one of the following three periodontal pathogens: Aa, Pg, or Bf. The number of target organisms per site was determined pre-operatively, at 1 week, and 1 month and 3 months postoperatively utilizing DNA probes. One quadrant in each patient was randomly assigned to each one of the following four treatment groups: 1) scaling and root planing (SRP group); 2) pocket reduction through osseous surgery and apically-positioned flap (OS group); 3) modified Widman flap (MWF group); and 4) modified Widman flap and topical application of saturated citric acid at pH 1 for 3 minutes (CA group). The 4 treatment modalities were performed in one appointment. No postoperative antibiotics were used. Patients were instructed to supplement their daily oral hygiene with chlorohexidine oral rinse during the study. The results of this investigation indicated that: 1) none of the treatment modalities was effective in eliminating the target species; 2) the incidence of infected sites for all groups was 100% preoperatively; 62.5%, 33.3%, and 31.3% at 1 week, and 1 and 3 months postoperatively, respectively; 3) these infected sites lost 1.1 +/- 0.4 mm of probing attachment compared to gain of 0.0 +/- 0.3 mm for uninfected sites; 4) the infected sites had higher plaque and bleeding on probing 0.9 +/- 0.3, 73 +/- 12%, respectively, compared to 0.3 +/- 0.1 and 30 +/- 8% for the uninfected sites

  5. Application of Bacteroides fragilis phage as an alternative indicator of sewage pollution in Tampa Bay, Florida

    USGS Publications Warehouse

    McLaughlin, M.R.; Rose, J.B.

    2006-01-01

    Traditional fecal coliform bacterial indicators have been found to be severely limited in determining the significance and sources of fecal contamination in ambient waters of tropical and subtropical regions. The bacteriophages that infect Bacteroides fragilis have been suggested as better fecal indicators and at least one type may be human specific. In this study, the phages that infect B. fragilis host RYC2056 (RYC), including phage B56-3, and host ATCC 51477-HSP40 (HSP), including the human specific phage B40-8, were evaluated in the drainage basins of Tampa Bay, 7 samples (n = 62), or 11%, tested positive for the presence of phages infecting the host HSP, whereas 28 samples, or 45%, tested positive using the host RYC. A survival study was also done to compare the persistence of phages B56-3 and B40-8 to MS2 coliphage in seawater at various temperatures. The decay rates for MS2 were 0.239 log 10 d-1 at 10??C, but increased to 0.896 at 20??C and 2.62 log10 d-1 at 30??C. The two B. fragilis phages persisted much longer in the seawater compared to the coliphage and showed little variation between the temperatures. All sewage influents sampled from area wastewater treatment plants contained phages that infected the two B. fragilis hosts at levels from 1.2 ?? 104 to 1.11 ?? 10 5 pfu 100 ml-1 for host RYC and 67 to 350 pfu 100 ml -1 for host HSP. Of the 7 chlorinated effluent samples tested, 3 were positive for the presence of the phage using the host RYC and the phage enrichment method, with levels estimated to be <10 pfu 100 ml-1. No phages were detected using the host HSP in the treated sewage effluent. Coliphages were found in 3 of the 7 effluent samples at a range of 30 to 1.2 ?? 103 pfu 100 ml-1. ?? 2006 Estuarine Research Federation.

  6. In vitro sulfotransferase activity of NodH, a nodulation protein of Rhizobium meliloti required for host-specific nodulation.

    PubMed Central

    Ehrhardt, D W; Atkinson, E M; Faull, K F; Freedberg, D I; Sutherlin, D P; Armstrong, R; Long, S R

    1995-01-01

    Early stages of nodulation involve the exchange of signals between the bacterium and the host plant. Bacterial nodulation (nod) genes are required for Rhizobium spp. to synthesize lipooligosaccharide morphogens, termed Nod factors. The common nod genes encode enzymes that synthesize the factor core structure, which is modified by host-specific gene products. Here we show direct in vitro evidence that Rhizobium meliloti NodH, a host-specific nodulation gene, catalyzes the transfer of sulfate from 3'-phosphoadenosine 5'-phosphosulfate to the terminal 6-O position of Nod factors, and we show substrate requirements for the reaction. Our results indicate that polymerization of the chitooligosaccharide backbone likely precedes sulfation and that sulfation is not absolutely dependent on the presence or the particular structure of the N-acyl modification. NodH sulfation provides a tool for the enzymatic in vitro synthesis of novel Nod factors, or putative Nod factors intermediates, with high specific activity. PMID:7592390

  7. Dual inoculation with an Aarbuscular Mycorrhizal fungus and Rhizobium to facilitate the growth of alfalfa on coal mine substrates

    SciTech Connect

    Wu, F.Y.; Bi, Y.L.; Wong, M.H.

    2009-07-01

    A pot experiment was conducted to investigate the effects of Glomus mosseae and Rhizobium on Medicago sativa grown on three types of coal mine substrates, namely a mixture of coal wastes and sands (CS), coal wastes and fly ash (CF), and fly ash (FA). Inoculation with Rhizobium alone did not result in any growth response but G. mosseae alone displayed a significant effect on plant growth. G. mosseae markedly increased the survival rate of M. sativa in CS substrate. In CF and FA substrates the respective oven dry weights of M. sativa inoculated with G. mosseae were 1.8 and 5.1 times higher than those without inoculation. Based on nitrogen (N), phosphorus (P) and potassium (K) uptake and legume growth, the results also show that dual inoculation in CS and CF substrates elicited a synergistic effect. This indicates that inoculation with arbuscular mycorrhizal (AM) fungi may be a promising approach for revegetation of coal mine substrates.

  8. Inoculation of the nonlegume Capsicum annuum L. with Rhizobium strains. 2. Changes in sterols, triterpenes, fatty acids, and volatile compounds.

    PubMed

    Silva, Luís R; Azevedo, Jessica; Pereira, Maria J; Carro, Lorena; Velazquez, Encarna; Peix, Alvaro; Valentão, Patrícia; Andrade, Paula B

    2014-01-22

    Peppers (Capsicum spp.) are consumed worldwide, imparting flavor, aroma, and color to foods, additionally containing high concentrations of biofunctional compounds. This is the first report about the effect of the inoculation of two Rhizobium strains on sterols, triterpenes, fatty acids, and volatile compounds of leaves and fruits of pepper (Capsicum annuum L.) plants. Generally, inoculation with strain TVP08 led to the major changes, being observed a decrease of sterols and triterpenes and an increase of fatty acids, which are related to higher biomass, growth, and ripening of pepper fruits. The increase of volatile compounds may reflect the elicitation of plant defense after inoculation, since the content on methyl salicylate was significantly increased in inoculated material. The findings suggest that inoculation with Rhizobium strains may be employed to manipulate the content of interesting metabolites in pepper leaves and fruits, increasing potential health benefits and defense abilities of inoculated plants. PMID:24405510

  9. Mimosine, a Toxin Present in Leguminous Trees (Leucaena spp.), Induces a Mimosine-Degrading Enzyme Activity in Some Rhizobium Strains

    PubMed Central

    Soedarjo, Muchdar; Hemscheidt, Thomas K.; Borthakur, Dulal

    1994-01-01

    Thirty-seven Rhizobium isolates obtained from the nodules of leguminous trees (Leucaena spp.) were selected on the basis of their ability to catabolize mimosine, a toxin found in large quantities in the seeds, foliage, and roots of plants of the genera Leucaena and Mimosa. A new medium containing mimosine as the sole source of carbon and nitrogen was used for selection. The enzymes of the mimosine catabolic pathway were inducible and were present in the soluble fraction of the cell extract of induced cells. On the basis of a comparison of the growth rates of Rhizobium strains on general carbon and nitrogen sources versus mimosine, the toxin appears to be converted mostly to biomass and carbon dioxide. Most isolates able to grow on mimosine as a source of carbon and nitrogen are also able to utilize 3-hydroxy-4-pyridone, a toxic intermediate of mimosine degradation in other organisms. PMID:16349454

  10. Interaction Between the Biotin Carboxyl Carrier Domain and the Biotin Carboxylase Domain in Pyruvate Carboxylase from Rhizobium etli†

    PubMed Central

    Lietzan, Adam D.; Menefee, Ann L.; Zeczycki, Tonya N.; Kumar, Sudhanshu; Attwood, Paul V.; Wallace, John C.; Cleland, W. Wallace; Maurice, Martin St.

    2011-01-01

    Pyruvate carboxylase (PC) catalyzes the ATP-dependent carboxylation of pyruvate to oxaloacetate, an important anaplerotic reaction in mammalian tissues. To effect catalysis, the tethered biotin of PC must gain access to active sites in both the biotin carboxylase domain and the carboxyl transferase domain. Previous studies have demonstrated that a mutation of threonine 882 to alanine in PC from Rhizobium etli renders the carboxyl transferase domain inactive and favors the positioning of biotin in the biotin carboxylase domain. We report the 2.4 Å resolution X-ray crystal structure of the Rhizobium etli PC T882A mutant which reveals the first high-resolution description of the domain interaction between the biotin carboxyl carrier protein domain and the biotin carboxylase domain. The overall quaternary arrangement of Rhizobium etli PC remains highly asymmetrical and is independent of the presence of allosteric activator. While biotin is observed in the biotin carboxylase domain, its access to the active site is precluded by the interaction between Arg353 and Glu248, revealing a mechanism for regulating carboxybiotin access to the BC domain active site. The binding location for the biotin carboxyl carrier protein domain demonstrates that tethered biotin cannot bind in the biotin carboxylase domain active site in the same orientation as free biotin, helping to explain the difference in catalysis observed between tethered biotin and free biotin substrates in biotin carboxylase enzymes. Electron density located in the biotin carboxylase domain active site is assigned to phosphonoacetate, offering a probable location for the putative carboxyphosphate intermediate formed during biotin carboxylation. The insights gained from the T882A Rhizobium etli PC crystal structure provide a new series of catalytic snapshots in PC and offer a revised perspective on catalysis in the biotin-dependent enzyme family. PMID:21958016

  11. Structure-Function Analysis of Nod Factor-Induced Root Hair Calcium Spiking in Rhizobium-Legume Symbiosis1

    PubMed Central

    Wais, Rebecca J.; Keating, David H.; Long, Sharon R.

    2002-01-01

    In the Rhizobium-legume symbiosis, compatible bacteria and host plants interact through an exchange of signals: Host compounds promote the expression of bacterial biosynthetic nod (nodulation) genes leading to the production of a lipochito-oligosaccharide signal, the Nod factor (NF). The particular array of nod genes carried by a given species of Rhizobium determines the NF structure synthesized and defines the range of legume hosts by which the bacterium is recognized. Purified NF can induce early host responses even in the absence of live Rhizobium One of the earliest known host responses to NF is an oscillatory behavior of cytoplasmic calcium, or calcium spiking, in root hair cells, initially observed in Medicago spp. and subsequently characterized in four other genera (D.W. Ehrhardt, R. Wais, S.R. Long [1996] Cell 85: 673–681; S.A. Walker, V. Viprey, J.A. Downie [2000] Proc Natl Acad Sci USA 97: 13413–13418; D.W. Ehrhardt, J.A. Downie, J. Harris, R.J. Wais, and S.R. Long, unpublished data). We sought to determine whether live Rhizobium trigger a rapid calcium spiking response and whether this response is NF dependent. We show that, in the Sinorhizobium meliloti-Medicago truncatula interaction, bacteria elicit a calcium spiking response that is indistinguishable from the response to purified NF. We determine that calcium spiking is a nod gene-dependent host response. Studies of calcium spiking in M. truncatula and alfalfa (Medicago sativa) also uncovered the possibility of differences in early NF signal transduction. We further demonstrate the sufficiency of the nod genes for inducing calcium spiking by using Escherichia coli BL21 (DE3) engineered to express 11 S. meliloti nod genes. PMID:12011352

  12. Evolutionary genetics and biogeographic structure of Rhizobium gallicum sensu lato, a widely distributed bacterial symbiont of diverse legumes.

    PubMed

    Silva, Claudia; Vinuesa, Pablo; Eguiarte, Luis E; Souza, Valeria; Martínez-Romero, Esperanza

    2005-11-01

    We used phylogenetic and population genetics approaches to evaluate the importance of the evolutionary forces on shaping the genetic structure of Rhizobium gallicum and related species. We analysed 54 strains from several populations distributed in the Northern Hemisphere, using nucleotide sequences of three 'core' chromosomal genes (rrs, glnII and atpD) and two 'auxiliary' symbiotic genes (nifH and nodB) to elucidate the biogeographic history of the species and symbiotic ecotypes (biovarieties) within species. The analyses revealed that strains classified as Rhizobium mongolense and Rhizobium yanglingense belong to the chromosomal evolutionary lineage of R. gallicum and harbour symbiotic genes corresponding to a new biovar; we propose their reclassification as R. gallicum bv. orientale. The comparison of the chromosomal and symbiotic genes revealed evidence of lateral transfer of symbiotic information within and across species. Genetic differentiation analyses based on the chromosomal protein-coding genes revealed a biogeographic pattern with three main populations, whereas the 16S rDNA sequences did not resolve that biogeographic pattern. Both the phylogenetic and population genetic analyses showed evidence of recombination at the rrs locus. We discuss our results in the light of the contrasting views of bacterial species expressed by microbial taxonomist and evolutionary biologists. PMID:16262857

  13. Two rhizobacterial strains, individually and in interactions with Rhizobium sp., enhance fusarial wilt control, growth, and yield in pigeon pea.

    PubMed

    Dutta, Swarnalee; Morang, Pranjal; Kumar S, Nishanth; Dileep Kumar, B S

    2014-09-01

    A Pseudomonas aeruginosa strain, RRLJ 04, and a Bacillus cereus strain, BS 03, were tested both individually and in combination with a Rhizobium strain, RH 2, for their ability to enhance plant growth and nodulation in pigeon pea (Cajanus cajan L.) under gnotobiotic, greenhouse and field conditions. Both of the rhizobacterial strains exhibited a positive effect on growth in terms of shoot height, root length, fresh and dry weight, nodulation and yield over the non-treated control. Co-inoculation of seeds with these strains and Rhizobium RH 2 also reduced the number of wilted plants, when grown in soil infested with Fusarium udum. Gnotobiotic studies confirmed that the suppression of wilt disease was due to the presence of the respective PGPR strains. Seed bacterization with drug-marked mutants of RRLJ 04 and BS 03 confirmed their ability to colonize and multiply along the roots. The results suggest that co-inoculation of these strains with Rhizobium strain RH 2 can be further exploited for enhanced growth, nodulation and yield in addition to control of fusarial wilt in pigeon pea. PMID:25224506

  14. Structural analysis of the genes encoding the molybdenum-iron protein of nitrogenase in the Parasponia rhizobium strain ANU289.

    PubMed Central

    Weinman, J J; Fellows, F F; Gresshoff, P M; Shine, J; Scott, K F

    1984-01-01

    The genes encoding the Molybdenum-Iron protein component of nitrogenase (nifD and nifK) have been identified and fully characterised in the Parasponia Rhizobium strain ANU289. The two genes are contiguous and are separated from the gene encoding the Fe-protein component of nitrogenase (nifH) by 21 kb of DNA. We present the entire DNA sequence of the nifD and nifK genes, thus completing the characterisation of the primary structure of the nitrogenase genes in this Rhizobium strain. Comparison of the sequence preceding the transcription initiation point of nifDK with that preceding nifH reveals a consensus promoter sequence 5'-PyTGGCAPyG-4 bp-TTGC(T/A)-10 bp-3'. This consensus promoter is found preceding nif genes in both fast-growing and slow-growing Rhizobium strains and shows a structural similarity to that preceding the coordinately-regulated nif operons in the asymbiotic organism Klebsiella pneumoniae. Images PMID:6095197

  15. Multilocus sequence analysis of Brazilian Rhizobium microsymbionts of common bean (Phaseolus vulgaris L.) reveals unexpected taxonomic diversity.

    PubMed

    Ribeiro, Renan Augusto; Barcellos, Fernando Gomes; Thompson, Fabiano L; Hungria, Mariangela

    2009-05-01

    The diazotrophic bacteria collectively known as "rhizobia" are important for establishing symbiotic N(2)-fixing associations with many legumes. These microbes have been used for over a century as an environmentally beneficial and cost-effective means of ensuring acceptable yields of agricultural legumes. The most widely used phylogenetic marker for identification and classification of rhizobia has been the 16S rRNA gene; however, this marker fails to discriminate some closely related species. In this study, we established the first multilocus sequence analysis (MLSA) scheme for the identification and classification of rhizobial microsymbionts of common bean (Phaseolus vulgaris L.). We analyzed 12 Brazilian strains representative of a collection of over 850 isolates in addition to type and reference rhizobial strains, by sequencing recA, dnaK, gltA, glnII and rpoA genes. Gene sequence similarities among the five type/reference Rhizobium strains which are symbionts of common bean ranged from 95 to 100% for 16S rRNA, and from 83 to 99% for the other five genes. Rhizobial species described as symbionts of common bean also formed separate groups upon analysis of single and concatenated gene sequences, and clusters formed in each tree were in good mutual agreement. The five additional loci may thus be considered useful markers of the genus Rhizobium; in addition, MLSA also revealed broad genetic diversity among strains classified as Rhizobium tropici, providing evidence of new species. PMID:19403105

  16. Pirin-like proteins are regulated by oxidative stress and iron in bacteroides fragilis and involved in the modulation of central energy metabolism and metronidazole susceptibility

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bacteroides fragilis is the most frequent anaerobe isolated from human infections. Clinical isolates of B. fragilis are among the highest aerotolerant anaerobic bacteria. The oxidative stress response (OSR) in B. fragilis induces an array of genes enabling them to survive prolonged oxygen exposure i...

  17. Draft Genome Sequence of "Candidatus Bacteroides periocalifornicus," a New Member of the Bacteriodetes Phylum Found within the Oral Microbiome of Periodontitis Patients.

    PubMed

    McLean, Jeffrey S; Liu, Quanhui; Thompson, John; Edlund, Anna; Kelley, Scott

    2015-01-01

    Here we present the draft genome of a distantly related member within the phylum Bacteriodetes, "Candidatus Bacteroides periocalifornicus." The draft genome sequence was assembled with metagenomic data from a patient with periodontitis. The closest relative has less than 68% average nucleic identity, supporting a novel family within Bacteriodetes. PMID:26701081

  18. Draft Genome Sequence of “Candidatus Bacteroides periocalifornicus,” a New Member of the Bacteriodetes Phylum Found within the Oral Microbiome of Periodontitis Patients

    PubMed Central

    Liu, Quanhui; Thompson, John; Edlund, Anna

    2015-01-01

    Here we present the draft genome of a distantly related member within the phylum Bacteriodetes, “Candidatus Bacteroides periocalifornicus.” The draft genome sequence was assembled with metagenomic data from a patient with periodontitis. The closest relative has less than 68% average nucleic identity, supporting a novel family within Bacteriodetes. PMID:26701081

  19. Probabilistic analysis showing that a combination of bacteroides and methanobrevibacter source tracking markers is effective for identifying waters contaminated by human fecal pollution

    USGS Publications Warehouse

    Johnston, Christopher; Byappanahalli, Muruleedhara N.; Gibson, Jacqueline MacDonald; Ufnar, Jennifer A.; Whitman, Richard L.; Stewart, Jill R.

    2013-01-01

    Microbial source tracking assays to identify sources of waterborne contamination typically target genetic markers of host-specific microorganisms. However, no bacterial marker has been shown to be 100% host-specific, and cross-reactivity has been noted in studies evaluating known source samples. Using 485 challenge samples from 20 different human and animal fecal sources, this study evaluated microbial source tracking markers including the Bacteroides HF183 16S rRNA, M. smithii nifH, and Enterococcus esp gene targets that have been proposed as potential indicators of human fecal contamination. Bayes' Theorem was used to calculate the conditional probability that these markers or a combination of markers can correctly identify human sources of fecal pollution. All three human-associated markers were detected in 100% of the sewage samples analyzed. Bacteroides HF183 was the most effective marker for determining whether contamination was specifically from a human source, and greater than 98% certainty that contamination was from a human source was shown when both Bacteroides HF183 and M. smithii nifH markers were present. A high degree of certainty was attained even in cases where the prior probability of human fecal contamination was as low as 8.5%. The combination of Bacteroides HF183 and M. smithii nifH source tracking markers can help identify surface waters impacted by human fecal contamination, information useful for prioritizing restoration activities or assessing health risks from exposure to contaminated waters.

  20. Near-complete genome sequence of the cellulolytic Bacterium Bacteroides (Pseudobacteroides) cellulosolvens ATCC 35603

    SciTech Connect

    Dassa, Bareket; Utturkar, Sagar M.; Hurt, Richard A.; Klingeman, Dawn Marie; Keller, Martin; Xu, Jian; Reddy, Harish Kumar; Borovok, Ilya; Grinberg, Inna Rozman; Lamed, Raphael; Zhivin, Olga; Bayer, Edward A.; Brown, Steven D.

    2015-09-24

    We report the single-contig genome sequence of the anaerobic, mesophilic, cellulolytic bacterium, Bacteroides cellulosolvens. The bacterium produces a particularly elaborate cellulosome system, whereas the types of cohesin-dockerin interactions are opposite of other known cellulosome systems: cell-surface attachment is thus mediated via type-I interactions whereas enzymes are integrated via type-II interactions.

  1. Xylan-regulated Delivery of Human Keratinocyte Growth Factor-2 to the Inflamed Colon by the Human Anaerobic Commensal Bacterium Bacteroides ovatus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The use of genetically modified bacteria to deliver biologically active molecules directly to the gut has become an increasingly attractive area of investigation. The challenge of regulation of production of the therapeutic molecule and colonization of the bowel led us to investigate Bacteroides ov...

  2. Lack of specificity for PCR assays targeting human Bacteroides 16S rRNA gene: cross-amplification with fish feces

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Methods focused on members of the genus Bacteroides have been increasingly utilized in microbial source tracking studies for identifying and quantifying sources of non-point fecal contamination. We present results using real-time PCR to show significant cross-amplification of a human-specific Bacter...

  3. Bacteroides isolated from four mammalian hosts lack host-specific 16S rRNA gene phylogeny and carbon and nitrogen utilization patterns*

    PubMed Central

    Atherly, Todd; Ziemer, Cherie J

    2014-01-01

    One-hundred-and-three isolates of Bacteroides ovatus,B. thetaiotaomicron, and B. xylanisolvens were recovered from cow, goat, human, and pig fecal enrichments with cellulose or xylan/pectin. Isolates were compared using 16S rRNA gene sequencing, repetitive sequence-based polymerase chain reaction (rep-PCR), and phenotypic microarrays. Analysis of 16S rRNA gene sequences revealed high sequence identity in these Bacteroides; with distinct phylogenetic groupings by bacterial species but not host origin. Phenotypic microarray analysis demonstrated these Bacteroides shared the ability to utilize many of the same carbon substrates, without differences due to species or host origin, indicative of their broad carbohydrate fermentation abilities. Limited nitrogen substrates were utilized; in addition to ammonia, guanine, and xanthine, purine derivatives were utilized by most isolates followed by a few amino sugars. Only rep-PCR analysis demonstrated host-specific patterns, indicating that genomic changes due to coevolution with host did not occur by mutation in the 16S rRNA gene or by a gain or loss of carbohydrate utilization genes within these Bacteroides. This is the first report to indicate that host-associated genomic differences are outside of 16S rRNA gene and carbohydrate utilization genes and suggest conservation of specific bacterial species with the same functionality across mammalian hosts for this Bacteroidetes clade. PMID:24532571

  4. THE PRIMARY STARCH UTILIZATION OPERON IN THE OBLIGATE ANAEROBE BACTEROIDES FRAGILIS IS REGULATED BY CARBON SOURCE AND OXYGEN, AND EXPRESSION IS IMPORTANT FOR SURVIVAL DURING OXIDATIVE STRESS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The obligate anaerobe Bacteroides fragilis is a commensal organism of the human large intestine where it utilizes both dietary and host-derived polysaccharides as a source of carbon and energy. This study describes the characterization of a novel operon, designated oxygen-induced starch utilization...

  5. Bacteroides propionicifaciens sp. nov., isolated from rice-straw residue in a methanogenic reactor treating waste from cattle farms.

    PubMed

    Ueki, Atsuko; Abe, Kunihiro; Kaku, Nobuo; Watanabe, Kazuya; Ueki, Katsuji

    2008-02-01

    Two strictly anaerobic bacterial strains (SV434(T) and S562) were isolated from rice-straw residue in a methanogenic reactor treating waste from cattle farms in Japan. They had identical 16S rRNA gene sequences and showed almost the same phenotypic properties. The cells of both strains were Gram-negative, non-motile, non-spore-forming rods; extraordinarily long rods often occurred. Remarkable stimulation of growth occurred with the addition of haemin and cobalamin (vitamin B(12)) to the medium. The supplementary cobalamin and haemin could be replaced if autoclaved and clarified sludge fluid obtained from the reactor was added. Both strains utilized a range of growth substrates, including arabinose, fructose, galactose, glucose, mannose, cellobiose, maltose, glycogen, starch, dextrin, amygdalin, lactate and pyruvate. Both strains produced acetate and propionate with a small amount of succinate from these substrates in the presence of haemin and cobalamin. Both strains were slightly alkaliphilic, having a pH optimum at about 7.9. The temperature range for growth was 5-35 degrees C, the optimum being 30 degrees C. The NaCl concentration range for growth was 0-4 % (w/v). Catalase activity was not detected in cells cultivated without haemin, whereas cells cultivated with haemin usually had the enzyme activity. Oxidase and nitrate-reducing activities were not detected. Aesculin was hydrolysed, but gelatin was not hydrolysed. Both strains were sensitive to bile acids. The major cellular fatty acids of both strains were anteiso-C(15 : 0) and iso-C(15 : 0). Menaquinones MK-8(H(0)) and MK-9(H(0)) were the major respiratory quinones and the genomic DNA G+C contents were 46.2-47.5 mol%. A phylogenetic analysis based on 16S rRNA gene sequences placed both strains in the phylum Bacteroidetes. Bacteroides coprosuis (isolated from swine-manure storage pits) was the species most closely related to both strains (95.9 % 16S rRNA gene sequence similarity to the type strain). On the

  6. Structure and sequence analyses of Bacteroides proteins BVU_4064 and BF1687 reveal presence of two novel predominantly-beta domains, predicted to be involved in lipid and cell surface interactions

    DOE PAGESBeta

    Natarajan, Padmaja; Punta, Marco; Kumar, Abhinav; Yeh, Andrew P; Godzik, Adam; Aravind, L.

    2015-01-16

    N-terminal domains of BVU_4064 and BF1687 proteins from Bacteroides vulgatus and Bacteroides fragilis respectively are members of the Pfam family PF12985 (DUF3869). Proteins containing a domain from this family can be found in most Bacteroides species and, in large numbers, in all human gut microbiome samples. Both BVU_4064 and BF1687 proteins have a consensus lipobox motif implying they are anchored to the membrane, but their functions are otherwise unknown. The C-terminal half of BVU_4064 is assigned to protein family PF12986 (DUF3870); the equivalent part of BF1687 was unclassified.

  7. New Degenerate Cytophaga-Flexibacter-Bacteroides-Specific 16S Ribosomal DNA-Targeted Oligonucleotide Probes Reveal High Bacterial Diversity in River Taff Epilithon

    PubMed Central

    O’Sullivan, Louise A.; Weightman, Andrew J.; Fry, John C.

    2002-01-01

    River microbial communities play an important role in global nutrient cycles, and aggregated bacteria such as those in epilithic biofilms may be major contributors. In this study the bacterial diversity of River Taff epilithon in South Wales was investigated. A 16S ribosomal DNA (rDNA) clone library was constructed and analyzed by partial sequencing of 76 of 347 clones and hybridization with taxon-specific probes. The epilithon was found to be very diverse, with an estimated 59.6% of the bacterial populations not accounted for by these clones. Members of the Cytophaga-Flexibacter-Bacteroides division (CFBs) were most abundant in the library, representing 25% of clones, followed by members of the α subdivision of the division Proteobacteria (α-Proteobacteria), γ-Proteobacteria, gram-positive bacteria, Cyanobacteria, β-Proteobacteria, δ-Proteobacteria, and the Prosthecobacter group. This study concentrated on the epilithic CFB populations, and a new set of degenerate 16S rDNA probes was developed to enhance their detection, namely, CFB560, CFB562, and CFB376. The commonly used probe CF319a/b may frequently lead to the underestimation of CFB populations in environmental studies, because it does not fully detect members of the division. CFB560 had exact matches to 95.6% of CFBs listed in the Ribosomal Database Project (release 8.0) small-subunit phylogenetic trees, compared to 60% for CF319a/b. The CFB probes detected 66 of 347 epilithon TAF clones, and 60 of these were partially sequenced. They affiliated with the RDP-designated groups Cytophaga, Sphingobacterium, Lewinella, and Cytophaga aurantiaca. CFB560 and CF319a/b detected 94% (62 of 66) and 48.5% (32 of 66) of clones, respectively, and therefore CFB560 is recommended for future use. Probe design in this study illustrated that multiple degenerate positions can greatly increase target range without adversely effecting specificity or experimental performance. PMID:11772628

  8. Isolation and the interaction between a mineral-weathering Rhizobium tropici Q34 and silicate minerals.

    PubMed

    Wang, Rong Rong; Wang, Qi; He, Lin Yan; Qiu, Gang; Sheng, Xia Fang

    2015-05-01

    The purposes of this study were to isolate and evaluate the interaction between mineral-weathering bacteria and silicate minerals (feldspar and biotite). A mineral-weathering bacterium was isolated from weathered rocks and identified as Rhizobium tropici Q34 based on 16S rRNA gene sequence analysis. Si and K concentrations were increased by 1.3- to 4.0-fold and 1.1- to 1.7-fold in the live bacterium-inoculated cultures compared with the controls respectively. Significant increases in the productions of tartaric and succinic acids and extracellular polysaccharides by strain Q34 were observed in cultures with minerals. Furthermore, significantly more tartaric acid and polysaccharide productions by strain Q34 were obtained in the presence of feldspar, while better growth and more citric acid production of strain Q34 were observed in the presence of biotite. Mineral dissolution experiments showed that the organic acids and polysaccharides produced by strain Q34 were also capable of promoting the release of Si and K from the minerals. The results showed that the growth and metabolite production of strain Q34 were enhanced in the presence of the minerals and different mineral exerted distinct impacts on the growth and metabolite production. The bio-weathering process is probably a synergistic action of organic acids and extracellular polysaccharides produced by the bacterium. PMID:25716616

  9. Molecular phylogenetic analysis of Rhizobium sullae isolated from Algerian Hedysarum flexuosum.

    PubMed

    Aliliche, Khadidja; Beghalem, Hamida; Landoulsi, Ahmed; Chriki, Ali

    2016-07-01

    Isolates from root nodules of Hedysarum flexuosum, sampled from north region of Algeria, were analyzed on the basis of their phenotypic and molecular characteristics. They were tested for their tolerance to NaCl, pH, temperatures, antibiotics and heavy metals resistance. Interestingly, the isolate Hf_04N appeared resistant to ZnCl2 (50 μg/mL) and grew at high saline concentration up to 9 %. The phylogenetic positions of five isolates were studied by comparative sequence analysis of 16S rRNA, recA, nifH and nodD genes. There were grouped close to the Rhizobium sullae type strain in relation to their 16S rRNA, recA and nifH genes-based phylogenies. By contrast, the tree of nodD gene was not congruent with ribosomal, housekeeping and nitrogen fixation genes. We suggest that our strains have a novel nodD gene. The detection of conserved domains of NodD protein and nitrogenase reductase enzyme, confirm their ability to nodulate and fix nitrogen. PMID:27034287

  10. Nitrogenase activity in Trifolium subterraneum L. in relation to the uptake of nitrate ions. [Rhizobium trifolii

    SciTech Connect

    Silsbury, J.H.

    1987-07-01

    An experiment was conducted to test the hypothesis that, when nitrogenase and nitrate reductase both contribute to the nitrogen nutrition of a nodulated legume, nitrogenase activity is inversely proportional to the rate of accumulation of organic nitrogen derived from the reduction of nitrate. Trifolium subterraneum L. plants, inoculated with Rhizobium trifolii and sown as small swards, were allowed to establish a closed canopy and steady rates of growth, dinitrogen fixation, and nitrogen accumulation. Swards were then supplied with nutrient solutions of 0, 0.5, 1.0, or 2.5 mM NO/sub 3//sup -/ with a 29.69% enrichment of /sup 15/N and allowed to grow for a further 33 days. Harvests were made to measure dry weight, nitrogen accumulation, /sup 15/N accumulation, NO/sub 3//sup -/ content and nitrogenase activity by acetylene reduction assay. Since the /sup 15/N of the plant organic matter could have been derived only from the NO/sub 3//sup -/ of the nutrient solution, its rate of accumulation provided a measure of the rate of NO/sub 3//sup -/ reduction. It was found that as this rate increased in response to external NO/sub 3//sup -/ concentration the rate of nitrogenase activity decreased proportionately. It is concluded that the reduction of nitrate and the reduction of dinitrogen act in a complementary manner to supply a plant with organic nitrogen for growth.

  11. Osmotic control of glycine betaine biosynthesis and degradation in Rhizobium meliloti

    SciTech Connect

    Smith, L.T.; Pocard, J.A.; Bernard, T.; Le Rudulier, D.

    1988-07-01

    Intracellular accumulation of glycine betaine has been shown to confer an enhanced level of osmotic stress tolerance in Rhizobium meliloti. In this study, the authors used a physiological approach to investigate the mechanism by which glycine betaine is accumulated in osmotically stressed R. meliloti. Results from growth experiments, /sup 14/C labeling of intermediates, and enzyme activity assays are presented. The results provide evidence for the pathway of biosynthesis and degradation of glycine betaine and the osmotic effects on this pathway. High osmolarity in the medium decreased the activities of the enzymes involved in the degradation of glycine betaine but not those of enzymes that lead to its biosynthesis from choline. Thus, the concentration of the osmoprotectant glycine betaine is increased in stressed cells. This report demonstrates the ability of the osmolarity of the growth medium to regulate the use of glycine betaine as a carbon and nitrogen source or as an osmoprotectant. The mechanisms of osmoregulation in R. meliloti and Escherichia coli are compared.

  12. Rhizobium Radiobacter Infection in a 27-Year-Old African American Woman With Munchausen Syndrome.

    PubMed

    Sawhney, Sameer; Naab, Tammey; Oneal, Partricia

    2016-08-01

    Rhizobium radiobacter is an opportunistic, usually saprophytic, gram-negative bacillus found in agricultural soil. Isolation from blood has been reported most often in hospitalized patients harboring malignant neoplasms or human immunodeficiency virus (HIV) associated immunosuppression, who have catheter or medical device-related febrile neutropenia; treatment involves removal of the catheter or implanted medical device.(1)Herein, we report a case of a 27-year-old African American woman with sickle cell anemia who sought treatment of generalized body pain, shaking, chills, dyspnea, and fever, suggestive of sickle cell crisis. As part of her work up, routine blood cultures were drawn, revealing the presence of a Gram negative bacillus that was identified as the nonfermenter bacillus R. radiobacter The patient displayed a unique infection with R. radiobacter sepsis in a patient secondary to self-injection of organic material into a peripheral line during hospitalization. The growth of an unusual organism in the blood of a patient, without the usual risk factors of R. radiobacter, raised suspicion of a factitious psychiatric disorder known as Munchausen syndrome, which was confirmed when we discovered self-injection of feces and dirt into a central intravenous (IV) line. PMID:27107290

  13. Symbiont abundance is more important than pre-infection partner choice in a Rhizobium - legume mutualism.

    PubMed

    Van Cauwenberghe, Jannick; Lemaire, Benny; Stefan, Andrei; Efrose, Rodica; Michiels, Jan; Honnay, Olivier

    2016-07-01

    It is known that the genetic diversity of conspecific rhizobia present in root nodules differs greatly among populations of a legume species, which has led to the suggestion that both dispersal limitation and the local environment affect rhizobial genotypic composition. However, it remains unclear whether rhizobial genotypes residing in root nodules are representative of the entire population of compatible symbiotic rhizobia. Since symbiotic preferences differ among legume populations, the genetic composition of rhizobia found within nodules may reflect the preferences of the local hosts, rather than the full diversity of potential nodulating rhizobia present in the soil. Here, we assessed whether Vicia cracca legume hosts of different provenances select different Rhizobium leguminosarum genotypes than sympatric V. cracca hosts, when presented a natural soil rhizobial population. Through combining V. cracca plants and rhizobia from adjacent and more distant populations, we found that V. cracca hosts are relatively randomly associated with rhizobial genotypes. This indicates that pre-infection partner choice is relatively weak in certain legume hosts when faced with a natural population of rhizobia. PMID:27269381

  14. Selecting Rhizobium meliloti for inoculation of alfalfa planted in acid soils

    SciTech Connect

    Lowendorf, H.S.; Alexander, M.

    1983-01-01

    The study was conducted to obtain Rhizobium meliloti strains suitable for use with alfalfa grown in acid soils. Thirteen strains of R. meliloti were examined for their ability to grow in acidified culture media and seven of these were characterized for the ability to surive in acid and limed nonsterile soils or grow in the presence of the host legume, Medicago sativa L. The pH values of the most acid, defined medium that permitted growth of the bacteria from a small inoculum ranged from pH 5.3 to 6.0. For R. meliloti 411SE1 and GH1-1SE1, the minimum pH that allowed for growth, the critical pH, was not a dependable indicator of survival in a more acid medium. Strains of R. meliloti with relatively low critical pH values survived better in a limed soil but not in acid soils than strains with higher critical pH values. Three strains of R. meliloti previously identified as good inoculants for alfalfa in acid soils did not consistently survive beter than other strains in a planted or unplanted acid soil of pH 5.3. However, the plants increase the population densities of these three strains more than other strains. These results suggest that R. meliloti strains suitable for inoculation of alfalfa in acid soils may be selected not by simple saprophytic properties but by their stimulation by the host legume in acid soils.

  15. Enhanced curdlan production with nitrogen feeding during polysaccharide synthesis by Rhizobium radiobacter.

    PubMed

    Wang, Xiao-Yu-Zhu; Dong, Jin-Jun; Xu, Guo-Chao; Han, Rui-Zhi; Ni, Ye

    2016-10-01

    Curdlan is a secondary metabolite synthesized by Agrobacterium sp. and some other bacteria. A newly isolated exopolysaccharide-producing strain was identified to be Rhizobium radiobacter CGMCC 12099. The polysaccharide product was confirmed to be curdlan with a molecule weight of 1.4×10(5)Da, and its molecular structure was determined by HPLC and infrared spectrum. Although nitrogen source is necessary for cell reproduction, curdlan production is largely dependent on nitrogen limitation, as well as cell vitality. Here, a nitrogen feeding strategy was investigated to elevate the curdlan production by R. radiobacter. The optimal concentration and addition time of (NH4)2HPO4 were investigated. The results showed that the enhanced cell density was correlated to the amount of (NH4)2HPO4 added. Also, nitrogen addition in earlier fermentation stage was beneficial to the cell growth and curdlan production. Furthermore, continuously feeding strategy was employed by feeding (NH4)2HPO4 at a constant rate of 1.24g/h at 35(th)h of fermentation for 9h, achieving a final curdlan production of 65.27g/L, productivity of 0.544g/L/h and glucose conversion rate of 38.89%. The curdlan production was improved by 2.1 times compared with that without nitrogen addition. This study provides a feasible and cheap nitrogen feeding strategy to enhance curdlan production. PMID:27312649

  16. Role of dark carbon dioxide fixation in root nodules of soybean. [Rhizobium japonicum

    SciTech Connect

    King, B.J.; Layzell, D.B.; Canvin, D.T.

    1986-05-01

    The magnitude and role of dark Co/sub 2/ fixation were examined in nodules of intact soybean plants (Harosoy 63 x Rhizobium japonicum strain USDA 16). The estimated rate of nodule dark CO/sub 2/ fixation, based on a 2 minute pulse-feed with /sup 14/CO/sub 2/ under saturating conditions, was 102 micromoles per gram dry weight per hour. This was equivalent to 14% of net nodule respiration. Only 18% of this CO/sub 2/ fixation was estimated to be required for organic and amino acid synthesis for growth and export processes. The major portion (75-92%) of fixed label was released as CO/sub 2/ within 60 minutes. The labeling pattern during pulse-chase experiments was consistent with CO/sub 2/ fixation by phosphoenolpyruvate carboxylase. During the chase, the greatest loss of label occurred in organic acids. Exposure of nodulated roots to Ar:O/sub 2/(80:20) did not affect dark CO/sub 2/ fixation, while exposure to O/sub 2/:CO/sub 2/(95:5) resulted in 54% inhibition. From these results, it was concluded that at least 66% of dark CO/sub 2/ fixation in soybean may be involved with the production of organic acids, which when oxidized would be capable of providing at least 48% of the requirement for ATP equivalents to support nitrogenase activity.

  17. Study of the basis for the competitiveness of Rhizobium japonicum in the nodulation of soybean

    SciTech Connect

    Bauer, W.

    1990-06-01

    The overall goal of our studies was to identify cellular and molecular characteristics of rhizobia that are important to root colonization and symbiotic infection in competition with indigenous soil microbes. Rhizobia were found to respond to specific host flavonoids as chemoattractants as well as nodulation gene inducers. Motility and chemotaxis contributed significantly to the efficiency of symbiotic interactions, but not to colonization of root tips, where bacterial dispersal depended primarily on passive movement by root cell elongation. Co-inoculation of Rhizobium nod gene mutants with each other and with the wild-type showed that the mutants could help the wild-type, but not each other, to initiate nodules. Mutants with defective host specificity genes were the only ones capable of helping the wild-type in an additive or synergistic manner. Alfalfa was shown to have rapid, systemic feedback regulation suppressing nodule formation in younger parts of the root system in response to initiation of the first nodules. Root mucilage and exudate components were found to affect attachment of rhizobia to root surfaces. Methods for optimal surface sterilization of legume seeds were examined. 5 refs.

  18. A second exopolysaccharide of Rhizobium meliloti strain SU47 that can function in root nodule invasion

    SciTech Connect

    Zhan, Hangjun; Levery, S.B.; Lee, C.C.; Leigh, J.A. )

    1989-05-01

    Rhizobium meliloti strain SU47 produces the calcofluor-binding exopolysaccharide, succinoglycan, that is required for alfalfa root nodule invasion. Strains derived from R. meliloti SU47 secreted an acidic exopolysaccharide, EPSb, that replaced succinoglycan in nodule invasion. EPSb, which has not formerly been identified among the Rhizobiaceae, consisted of the repeating unit 4,6-O-(1-carboxyethylidene)-{alpha}-D-Galp1{yields}3(X-O-Ac)-{beta}-D-Glcp1{yields}3. EPSb synthesis occurred either in strains containing a mutation in a locus designated mucR or in strains with a recombinant cosmid pMuc. mucR mapped slightly counterclockwise from pyr49 on the chromosome, while pMuc contained genes mapping to the megaplasmid pRmeSU47b. In exoA, -F, and -H mutants, which are deficient in normal succinoglycan secretion and nodule invasion, a transposon Tn5 insertion in mucR or the presence of pMuc resulted in EPSb secretion and a restoration of nodule invasion on Medicago sativa and Melilotus alba. Mutants in exoB and exoC were incapable of succinoglycan and EPSb secretion as well as nodule invasion. A mutant that secreted succinoglycan but was incapable of EPSb secretion invaded nodules normally.

  19. Cadmium resistance screening in nitrilotriacetate-buffered minimal media. [Rhizobium fredii

    SciTech Connect

    Angle, J.S. ); Chaney, R.L. )

    1989-08-01

    Media used to determine the MICs of heavy metals for bacteria are unreliable because organic components in the media bind or chelate most of the metal being studied. To define specific metal activity in media and to maintain metal activity at a constant level, HEPES-MES (N-2-hydroxyethylpiperazine-N{prime}-2-ethanesulfonic acid-2-(N-morpholine)ethanesulfonic acid) salts medium with arabinose medium was modified, and the modified medium was used to examine the MIC of cadmium for Rhizobium fredii USDA 201. Arabinose-HEPES-MES was modified by addition of the chelator nitrilotriacetate to buffer the supply of free Cd{sup 2+} ion to maintain a constant Cd activity and by the use of only MES to buffer pH (buffered arabinose-MES medium (BAM)). Ca and Mg were supplied at the normal levels for soil solutions, and other trace elements were supplied at the levels required for normal growth of plants. The concentration of free Cd{sup 2+} ion was calculated by using the computer program GEOCHEM-PC with a corrected data base. The Cd MIC in BAM was 14.0 {mu}M, while that in a tryptone-yeast extract medium was 107 {mu}M. The results indicate that substantial free Cd{sup 2+} is removed from solution in most standard media, resulting in falsely high MICs. The new BAM medium allows for the precise determination of MICs, thus avoiding the uncertainties associated with other media.

  20. Increased effectiveness of competitive rhizobium strains upon inoculation of Cajanus cajan

    SciTech Connect

    Hernandez, B.S.; Poth, M.; Focht, D.D.

    1987-09-01

    A field study was conducted in lysimeters containing /sup 15/N-enriched soil to determine the effects of four competitive rhizobium strains upon yield parameters of pigeon peas (Cajanus cajan). The greatest differences observed were in seed yields; strain P132 effected the highest seed yield (121 +/- 20 g per plant), and the control strain (indigenous rhizobia) effected the lowest yield (43.9 +/- 8 g per plant). With the exception of seeds and pods, the dry matter weights were not different. Although there appeared to be no effect by inoculum strains on the fractional content of N derived from biological nitrogen fixation when the total plant biomass was considered, strains P132 and 401 partitioned more of the N derived from fixation into seeds and leaves than did the other strains. Because the seeds comprised the major portion of plant N, more total N and more N derived from biological nitrogen fixation (about half of total N) were found in plants inoculated with P132, whereas the smallest amount was found in the uninoculated controls. P132 was also the best competitor with respect to indigenous rhizobia and accounted for all of the nodules found on the plants in which it was inoculated.

  1. Exopolysaccharide and Poly-(beta)-Hydroxybutyrate Coproduction in Two Rhizobium meliloti Strains

    PubMed Central

    Tavernier, P.; Portais, J.; Nava, Sa; Courtois, J.; Courtois, B.; Barbotin, J.

    1997-01-01

    The effects of different nitrogen and carbon sources on cell growth, pH, and exopolysaccharide (EPS) and poly-(beta)-hydroxybutyrate (PHB) production by two strains of Rhizobium meliloti (M5N1 and Su47) are reported. Differences in the behavior of glucose- and fructose-grown cells were shown, in particular with the M5N1 strain. Growth in a glucose-containing medium was accompanied by acidification of the culture medium, which leads to cell death. On fructose, acidification was detected only in the medium with a mineral nitrogen supply. A lag phase in EPS production was observed with cells grown with glucose, probably related to an initial extracellular conversion of the carbohydrate into an acid. No lag phase was observed in EPS production from fructose or in PHB synthesis whatever the carbon source. A decrease in PHB content was noticed for both strains under conditions where acidification of media occurred. The extent of production, emphasized by the use of a coproduction index, indicates that the M5N1 strain is a more promising organism than is the Su47 strain for polymer production. Such a strain, put in rich medium (containing yeast extract) supplemented with fructose, accumulated PHB up to 85% of dry cell weight and excreted about 1.5 g of EPS per liter in the medium. Regulation of the coproduction of EPS and PHB by these cells is suggested. PMID:16535485

  2. Excessive excretion of cyclic beta-(1,2)-glucan by Rhizobium trifolii TA-1.

    PubMed Central

    Breedveld, M W; Zevenhuizen, L P; Zehnder, A J

    1990-01-01

    At 25 degrees C, the optimal temperature for growth of Rhizobium trifolii TA-1, extracellular and capsular polysaccharide (EPS and CPS) were the main carbohydrate products synthesized in mannitol-rich medium (10 g of mannitol and 1 g of glutamic acid per liter). In the same medium at 33 degrees C, EPS and CPS production was inhibited, and up to 3.9 g of cyclic beta-(1,2)-glucan was produced during an incubation period of 20 days with a total biomass of 0.55 g of protein. In a medium containing 50 g of mannitol and 10 g of glutamic acid per liter, high cell densities (3.95 g of protein) were obtained at 25 degrees C. This biomass excreted 10.9 g of cyclic beta-(1,2)-glucan within 10 days. Concomitantly, 4.8 g of EPS were synthesized, while CPS production was strongly suppressed. The excreted cyclic beta-(1,2)-glucans were neutral and had degrees of polymerization ranging from 17 to 25, with a degree of polymerization of 19 as the major glucan cycle. PMID:2117876

  3. Characterization of polysaccharides of Rhizobium meliloti exo mutants that form ineffective nodules.

    PubMed Central

    Leigh, J A; Lee, C C

    1988-01-01

    Mutants of Rhizobium meliloti SU47 with defects in the production of the Calcofluor-binding expolysaccharide succinoglycan failed to gain entry into alfalfa root nodules. In order to define better the polysaccharide phenotypes of these exo mutants, we analyzed the periplasmic oligosaccharide cyclic (1-2)-beta-D-glucan and lipopolysaccharide (LPS) in representative mutants. The exoC mutant lacked the glucan and had abnormal LPS which appeared to lack a substantial portion of the O side chain. The exoB mutant had a spectrum of LPS species which differed from those of both the wild-type parental strain and the exoC mutant. The presence of the glucan and normal LPS in the exoA, exoD, exoF, and exoH mutants eliminated defects in these carbohydrates as explanations for the nodule entry defects of these mutants. We also assayed for high- and low-molecular-weight succinoglycans. All of the exo mutants except exoD and exoH completely lacked both forms. For the Calcofluor-dim exoD mutant, the distribution of high- and low-molecular-weight forms depended on the growth medium. The haloless exoH mutant produced high-molecular-weight and only a trace of low-molecular-weight succinoglycan; the succinyl modification was missing, as was expected from the results of previous studies. The implications of these observations with regard to nodule entry are discussed. Images PMID:3403505

  4. Species limits in Rhizobium populations that nodulate the common bean (Phaseolus vulgaris).

    PubMed Central

    Eardly, B D; Wang, F S; Whittam, T S; Selander, R K

    1995-01-01

    Evolutionary genetic relationships among 146 bean-nodulating Rhizobium strains, including 94 field isolates from three localities in Colombia and 36 strains from Mexico, were examined by multilocus enzyme electrophoresis and restriction fragment length polymorphism analysis of a PCR-amplified 260-bp segment of the 16S rRNA gene. Seventy-five electrophoretic types (ETs), corresponding to multilocus enzyme genotypes, were identified, including a genotypically diverse group of 18 ETs in Colombia that is strongly differentiated from the ETs of R. etli, which occur in Mexico, Colombia, and Brazil. Most strains of the distinctive Colombian ETs carried the same 16S rRNA allele as did strains of R. etli, but, surprisingly, 17 isolates of two of these ETs had the allele that is characteristic of R. leguminosarum, and strains of two other divergent groups of ETs were also polymorphic for the two alleles. No fully satisfactory explanation for the occurrence of the R. leguminosarum 16S rRNA allele in three distantly related groups of strains is available, but horizontal transfer and recombination of the gene, in whole or in part, would seem to be more plausible than convergence in nucleotide sequence. PMID:7574588

  5. Enzymatic tailoring of ornithine in the biosynthesis of the Rhizobium cyclic trihydroxamate siderophore vicibactin.

    PubMed

    Heemstra, John R; Walsh, Christopher T; Sattely, Elizabeth S

    2009-10-28

    To acquire iron, the N(2)-fixing, symbiotic bacterium Rhizobium sp. produce the cyclic trihydroxamate siderophore vicibactin, containing a 30-membered trilactone scaffold. Herein we report the overproduction and purification of the six proteins VbsACGOLS in the bacterial host Escherichia coli and the reconstitution of the biosynthesis of vicibactin from primary metabolites. The flavoprotein VbsO acts as a pathway-initiating l-ornithine N(5)-hydroxylase, followed by VbsA, which transfers (R)-3-hydroxybutyryl- from the CoA thioester to N(5)-hydroxyornithine to yield N(5)-((R)-3-hydroxybutyryl)-N(5)-hydroxy-l-ornithine. VbsL is a PLP-dependent epimerase acting at C(2) of the 10 atom monomer unit. VbsS, a nonribosomal peptide synthetase free-standing module, then activates N(5)-((R)-3-hydroxybutyryl)-N(5)-hydroxy-d-ornithine as the AMP anhydride on the way to cyclotrimerization to the vicibactin scaffold. The last step, tris-acetylation of the C(2) amino group of desacetyl-d-vicibactin to the mature siderophore vicibactin, is catalyzed distributively by VbsC, using three molecules of acetyl-CoA. PMID:19778043

  6. Rhizobium etli asparaginase II: an alternative for acute lymphoblastic leukemia (ALL) treatment.

    PubMed

    Huerta-Saquero, Alejandro; Evangelista-Martínez, Zahaed; Moreno-Enriquez, Angélica; Perez-Rueda, Ernesto

    2013-01-01

    Bacterial L-asparaginase has been a universal component of therapies for childhood acute lymphoblastic leukemia since the 1970s. Two principal enzymes derived from Escherichia coli and Erwinia chrysanthemi are the only options clinically approved to date. We recently reported a study of recombinant L-asparaginase (AnsA) from Rhizobium etli and described an increasing type of AnsA family members. Sequence analysis revealed four conserved motifs with notable differences with respect to the conserved regions of amino acid sequences of type I and type II L-asparaginases, particularly in comparison with therapeutic enzymes from E. coli and E. chrysanthemi. These differences suggested a distinct immunological specificity. Here, we report an in silico analysis that revealed immunogenic determinants of AnsA. Also, we used an extensive approach to compare the crystal structures of E. coli and E. chrysantemi asparaginases with a computational model of AnsA and identified immunogenic epitopes. A three-dimensional model of AsnA revealed, as expected based on sequence dissimilarities, completely different folding and different immunogenic epitopes. This approach could be very useful in transcending the problem of immunogenicity in two major ways: by chemical modifications of epitopes to reduce drug immunogenicity, and by site-directed mutagenesis of amino acid residues to diminish immunogenicity without reduction of enzymatic activity. PMID:22895060

  7. Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum

    PubMed Central

    Kumar, Nitin; Lad, Ganesh; Giuntini, Elisa; Kaye, Maria E.; Udomwong, Piyachat; Shamsani, N. Jannah; Young, J. Peter W.; Bailly, Xavier

    2015-01-01

    Biological species may remain distinct because of genetic isolation or ecological adaptation, but these two aspects do not always coincide. To establish the nature of the species boundary within a local bacterial population, we characterized a sympatric population of the bacterium Rhizobium leguminosarum by genomic sequencing of 72 isolates. Although all strains have 16S rRNA typical of R. leguminosarum, they fall into five genospecies by the criterion of average nucleotide identity (ANI). Many genes, on plasmids as well as the chromosome, support this division: recombination of core genes has been largely within genospecies. Nevertheless, variation in ecological properties, including symbiotic host range and carbon-source utilization, cuts across these genospecies, so that none of these phenotypes is diagnostic of genospecies. This phenotypic variation is conferred by mobile genes. The genospecies meet the Mayr criteria for biological species in respect of their core genes, but do not correspond to coherent ecological groups, so periodic selection may not be effective in purging variation within them. The population structure is incompatible with traditional ‘polyphasic taxonomy′ that requires bacterial species to have both phylogenetic coherence and distinctive phenotypes. More generally, genomics has revealed that many bacterial species share adaptive modules by horizontal gene transfer, and we envisage a more consistent taxonomic framework that explicitly recognizes this. Significant phenotypes should be recognized as ‘biovars' within species that are defined by core gene phylogeny. PMID:25589577

  8. Rhizobium leguminosarum HupE is a highly-specific diffusion facilitator for nickel uptake.

    PubMed

    Albareda, Marta; Rodrigue, Agnès; Brito, Belén; Ruiz-Argüeso, Tomás; Imperial, Juan; Mandrand-Berthelot, Marie-Andrée; Palacios, Jose

    2015-04-01

    Bacteria require nickel transporters for the synthesis of Ni-containing metalloenzymes in natural, low nickel habitats. In this work we carry out functional and topological characterization of Rhizobium leguminosarum HupE, a nickel permease required for the provision of this element for [NiFe] hydrogenase synthesis. Expression studies in the Escherichia coli nikABCDE mutant strain HYD723 revealed that HupE is a medium-affinity permease (apparent Km 227 ± 21 nM; Vmax 49 ± 21 pmol Ni(2+) min(-1) mg(-1) bacterial dry weight) that functions as an energy-independent diffusion facilitator for the uptake of Ni(ii) ions. This Ni(2+) transport is not inhibited by similar cations such as Mn(2+), Zn(2+), or Co(2+), but is blocked by Cu(2+). Analysis of site-directed HupE mutants allowed the identification of several residues (H36, D42, H43, F69, E90, H130, and E133) that are essential for HupE-mediated Ni uptake in E. coli cells. By using translational fusions to reporter genes we demonstrated the presence of five transmembrane domains with a periplasmic N-terminal domain and a C-terminal domain buried in the lipid bilayer. The periplasmic N-terminal domain contributes to stability and functionality of the protein. PMID:25652141

  9. Characterization of the Rhizobium (Sinorhizobium) meliloti high- and low-affinity phosphate uptake systems.

    PubMed Central

    Voegele, R T; Bardin, S; Finan, T M

    1997-01-01

    Genetic studies have suggested that Rhizobium (Sinorhizobium) meliloti contains two distinct phosphate (Pi) transport systems, encoded by the phoCDET genes and the orfA-pit genes, respectively. Here we present data which show that the ABC-type PhoCDET system has a high affinity for Pi (Km, 0.2 microM) and that Pi uptake by this system is severely inhibited by phosphonates. This high-affinity uptake system was induced under Pi-limiting conditions and was repressed in the presence of excess Pi. Uptake via the OrfA-Pit system was examined in (i) a phoC mutant which showed increased expression of the orfA-pit genes as a result of a promoter-up mutation and (ii) a phoB mutant (PhoB is required for phoCDET expression). Pi uptake in both strains exhibited saturation kinetics (Km, 1 to 2 microM) and was not inhibited by phosphonates. This uptake system was active in wild-type cells grown with excess Pi and appeared to be repressed when the cells were starved for Pi. Thus, our biochemical data show that the OrfA-Pit and PhoCDET uptake systems are differentially expressed depending on the state of the cell with respect to phosphate availability. PMID:9393684

  10. Narrow-Host-Range Bacteriophages That Infect Rhizobium etli Associate with Distinct Genomic Types

    PubMed Central

    Santamaría, Rosa Isela; Bustos, Patricia; Sepúlveda-Robles, Omar; Lozano, Luis; Rodríguez, César; Fernández, José Luis; Juárez, Soledad; Kameyama, Luis; Guarneros, Gabriel; Dávila, Guillermo

    2014-01-01

    In this work, we isolated and characterized 14 bacteriophages that infect Rhizobium etli. They were obtained from rhizosphere soil of bean plants from agricultural lands in Mexico using an enrichment method. The host range of these phages was narrow but variable within a collection of 48 R. etli strains. We obtained the complete genome sequence of nine phages. Four phages were resistant to several restriction enzymes and in vivo cloning, probably due to nucleotide modifications. The genome size of the sequenced phages varied from 43 kb to 115 kb, with a median size of ∼45 to 50 kb. A large proportion of open reading frames of these phage genomes (65 to 70%) consisted of hypothetical and orphan genes. The remainder encoded proteins needed for phage morphogenesis and DNA synthesis and processing, among other functions, and a minor percentage represented genes of bacterial origin. We classified these phages into four genomic types on the basis of their genomic similarity, gene content, and host range. Since there are no reports of similar sequences, we propose that these bacteriophages correspond to novel species. PMID:24185856

  11. Cloning of Rhizobium leguminosarum genes for competitive nodulation blocking on peas.

    PubMed Central

    Dowling, D N; Samrey, U; Stanley, J; Broughton, W J

    1987-01-01

    One type of competitive interaction among rhizobia is that between nonnodulating and nodulating strains of Rhizobium leguminosarum on primitive pea genotypes. Pisum sativum cv. Afghanistan nodulates effectively with R. leguminosarum TOM, and this can be blocked in mixed inoculations by R. leguminosarum PF2, which does not nodulate this cultivar. We termed this PF2 phenotype Cnb+, for competitive nodulation blocking. Strain PF2 contains three large plasmids including a 250-kilobase-pair symbiotic (Sym) plasmid. Transfer of this plasmid, pSymPF2, to nonblocking rhizobia conferred the Cnb+ phenotype on recipients in mixed inoculations on cultivar Afghanistan with TOM. A library of the PF2 genome constructed in the vector pMMB33 was used to isolate two cosmid clones which hybridize to pSymPF2. These cosmids, pDD50 and pDD58, overlapped to the extent of 23 kilobase pairs and conferred a Cnb+ phenotype on recipient Cnb- rhizobia, as did pSD1, a subclone from the common region. Images PMID:3546272

  12. Genomic and phenotypic characterization of Rhizobium gallicum phage vB_RglS_P106B.

    PubMed

    Halmillawewa, Anupama P; Restrepo-Córdoba, Marcela; Yost, Christopher K; Hynes, Michael F

    2015-03-01

    The phage P106B (vB_RglS_P106B) is a Siphoviridae phage with a narrow spectrum of infectivity, which has been isolated from soils with a history of pea cultivation. The trapping host of P106B is an indigenous strain of Rhizobium gallicum (SO14B-4) isolated from soils associated with Vicia cracca. Phenotypic characterization of the phage revealed that P106B has an approximate burst size of 21 p.f.u. per infected cell with 60 min and 100 min eclipse and latent periods, respectively. Phage P106B was unable to transduce under the conditions tested. The genome of P106B is 56 024 bp in length with a mean DNA G+C content of 47.9 %. The complete genome sequence contains 95 putative ORFs and a single tRNA gene coding for leucine with the anticodon TTA. Putative functions could only be assigned to 22 of the predicted ORFs while a significant number of ORFs (47) shared no sequence similarities to previously characterized proteins. The remaining 26 putative protein-coding genes exhibited a sequence resemblance to other hypothetical proteins. No lysogeny-related genes were found in the P106B genome. PMID:25627439

  13. Rhizobium sp. Strain NGR234 Possesses a Remarkable Number of Secretion Systems▿ †

    PubMed Central

    Schmeisser, Christel; Liesegang, Heiko; Krysciak, Dagmar; Bakkou, Nadia; Le Quéré, Antoine; Wollherr, Antje; Heinemeyer, Isabelle; Morgenstern, Burkhard; Pommerening-Röser, Andreas; Flores, Margarita; Palacios, Rafael; Brenner, Sydney; Gottschalk, Gerhard; Schmitz, Ruth A.; Broughton, William J.; Perret, Xavier; Strittmatter, Axel W.; Streit, Wolfgang R.

    2009-01-01

    Rhizobium sp. strain NGR234 is a unique alphaproteobacterium (order Rhizobiales) that forms nitrogen-fixing nodules with more legumes than any other microsymbiont. We report here that the 3.93-Mbp chromosome (cNGR234) encodes most functions required for cellular growth. Few essential functions are encoded on the 2.43-Mbp megaplasmid (pNGR234b), and none are present on the second 0.54-Mbp symbiotic plasmid (pNGR234a). Among many striking features, the 6.9-Mbp genome encodes more different secretion systems than any other known rhizobia and probably most known bacteria. Altogether, 132 genes and proteins are linked to secretory processes. Secretion systems identified include general and export pathways, a twin arginine translocase secretion system, six type I transporter genes, one functional and one putative type III system, three type IV attachment systems, and two putative type IV conjugation pili. Type V and VI transporters were not identified, however. NGR234 also carries genes and regulatory networks linked to the metabolism of a wide range of aromatic and nonaromatic compounds. In this way, NGR234 can quickly adapt to changing environmental stimuli in soils, rhizospheres, and plants. Finally, NGR234 carries at least six loci linked to the quenching of quorum-sensing signals, as well as one gene (ngrI) that possibly encodes a novel type of autoinducer I molecule. PMID:19376903

  14. A phosphate transport system is required for symbiotic nitrogen fixation by Rhizobium meliloti.

    PubMed Central

    Bardin, S; Dan, S; Osteras, M; Finan, T M

    1996-01-01

    The bacterium Rhizobium meliloti forms N2-fixing root nodules on alfalfa plants. The ndvF locus, located on the 1,700-kb pEXO megaplasmid of R. meliloti, is required for nodule invasion and N2 fixation. Here we report that ndvF contains four genes, phoCDET, which encode an ABC-type transport system for the uptake of Pi into the bacteria. The PhoC and PhoD proteins are homologous to the Escherichia coli phosphonate transport proteins PhnC and PhnD. The PhoT and PhoE proteins are homologous to each other and to the E. coli phosphonate transport protein PhnE. We show that the R. meliloti phoD and phoE genes are induced in response to phosphate starvation and that the phoC promoter contains two elements which are similar in sequence to the PHO boxes present in E. coli phosphate-regulated promoters. The R. meliloti ndvF mutants grow poorly at a phosphate concentration of 2 mM, and we hypothesize that their symbiotic phenotype results from their failure to grow during the nodule infection process. Presumably, the PhoCDET transport system is employed by the bacteria in the soil environment, where the concentration of available phosphate is normally 0.1 to 1 microM. PMID:8755882

  15. Hydroxylated ornithine lipids increase stress tolerance in Rhizobium tropici CIAT899

    PubMed Central

    Vences-Guzmán, Miguel Ángel; Guan, Ziqiang; Ormeño-Orrillo, Ernesto; González-Silva, Napoleón; López-Lara, Isabel M.; Martínez-Romero, Esperanza; Geiger, Otto; Sohlenkamp, Christian

    2011-01-01

    Ornithine lipids (OLs) are widespread among gram-negative bacteria. Their basic structure consists of a 3-hydroxy fatty acyl group attached in amide linkage to the α-amino group of ornithine and a second fatty acyl group ester-linked to the 3-hydroxy position of the first fatty acid. OLs can be hydroxylated within the secondary fatty acyl moiety and this modification has been related to increased stress tolerance. Rhizobium tropici, a nodule-forming α-proteobacterium known for its stress tolerance, forms four different OLs. Studies of the function of these OLs have been hampered due to lack of knowledge about their biosynthesis. Here we describe that OL biosynthesis increases under acid stress and that OLs are enriched in the outer membrane. Using a functional expression screen, the OL hydroxylase OlsE was identified, which in combination with the OL hydroxylase OlsC is responsible for the synthesis of modified OLs in R. tropici. Unlike described OL hydroxylations, the OlsE-catalyzed hydroxylation occurs within the ornithine moiety. Mutants deficient in OlsE or OlsC and double mutants deficient in OlsC/OlsE were characterized. R. tropici mutants deficient in OlsC-mediated OL hydroxylation are more susceptible to acid and temperature stress. All three mutants lacking OL hydroxylases are affected during symbiosis. PMID:21205018

  16. An empirical test of partner choice mechanisms in a wild legume–rhizobium interaction

    PubMed Central

    Simms, Ellen L; Taylor, D. Lee; Povich, Joshua; Shefferson, Richard P; Sachs, J.L; Urbina, M; Tausczik, Y

    2005-01-01

    Mutualisms can be viewed as biological markets in which partners of different species exchange goods and services to their mutual benefit. Trade between partners with conflicting interests requires mechanisms to prevent exploitation. Partner choice theory proposes that individuals might foil exploiters by preferentially directing benefits to cooperative partners. Here, we test this theory in a wild legume–rhizobium symbiosis. Rhizobial bacteria inhabit legume root nodules and convert atmospheric dinitrogen (N2) to a plant available form in exchange for photosynthates. Biological market theory suits this interaction because individual plants exchange resources with multiple rhizobia. Several authors have argued that microbial cooperation could be maintained if plants preferentially allocated resources to nodules harbouring cooperative rhizobial strains. It is well known that crop legumes nodulate non-fixing rhizobia, but allocate few resources to those nodules. However, this hypothesis has not been tested in wild legumes which encounter partners exhibiting natural, continuous variation in symbiotic benefit. Our greenhouse experiment with a wild legume, Lupinus arboreus, showed that although plants frequently hosted less cooperative strains, the nodules occupied by these strains were smaller. Our survey of wild-grown plants showed that larger nodules house more Bradyrhizobia, indicating that plants may prevent the spread of exploitation by favouring better cooperators. PMID:16519238

  17. Rhizobium meliloti produces a family of sulfated lipooligosaccharides exhibiting different degrees of plant host specificity.

    PubMed Central

    Schultze, M; Quiclet-Sire, B; Kondorosi, E; Virelizer, H; Glushka, J N; Endre, G; Géro, S D; Kondorosi, A

    1992-01-01

    We have shown that a Rhizobium meliloti strain overexpressing nodulation genes excreted high amounts of a family of N-acylated and 6-O-sulfated N-acetyl-beta-1,4-D-glucosamine penta-, tetra-, and trisaccharide Nod factors. Either a C(16:2) or a C(16:3) acyl chain is attached to the nonreducing end subunit, whereas the sulfate group is bound to the reducing glucosamine. One of the tetrasaccharides is identical to the previously described NodRm-1 factor. The two pentasaccharides as well as NodRm-1 were purified and tested for biological activity. In the root hair deformation assay the pentasaccharides show similar activities on the host plants Medicago sativa and Melilotus albus and on the non-host plant Vicia sativa at a dilution of up to 0.01-0.001 microM, in contrast to NodRm-1, which displays a much higher specific activity for Medicago and Melilotus than for Vicia. The active concentration range of the pentasaccharides is more narrow on Medicago than on Melilotus and Vicia. In addition to root hair deformation, the different Nod factors were shown to induce nodule formation on M. sativa. We suggest that the production of a series of active signal molecules with different degrees of specificity might be important in controlling the symbiosis of R. meliloti with several different host plants or under different environmental conditions. Images PMID:1729688

  18. Osmotic control of glycine betaine biosynthesis and degradation in Rhizobium meliloti.

    PubMed Central

    Smith, L T; Pocard, J A; Bernard, T; Le Rudulier, D

    1988-01-01

    Intracellular accumulation of glycine betaine has been shown to confer an enhanced level of osmotic stress tolerance in Rhizobium meliloti. In this study, we used a physiological approach to investigate the mechanism by which glycine betaine is accumulated in osmotically stressed R. meliloti. Results from growth experiments, 14C labeling of intermediates, and enzyme activity assays are presented. The results provide evidence for the pathway of biosynthesis and degradation of glycine betaine and the osmotic effects on this pathway. High osmolarity in the medium decreased the activities of the enzymes involved in the degradation of glycine betaine but not those of enzymes that lead to its biosynthesis from choline. Thus, the concentration of the osmoprotectant glycine betaine is increased in stressed cells. This report demonstrates the ability of the osmolarity of the growth medium to regulate the use of glycine betaine as a carbon and nitrogen source or as an osmoprotectant. The mechanisms of osmoregulation in R. meliloti and Escherichia coli are compared. PMID:3290197

  19. Quantitative comparison of the laboratory and field competitiveness of Rhizobium leguminosarum biovar phaseoli.

    PubMed

    Beattie, G A; Clayton, M K; Handelsman, J

    1989-11-01

    Rhizobium leguminosarum bv. phaseoli KIM5s outcompeted strain CE3 in bean (Phaseolus vulgaris L.) root nodulation when plants were grown at any of three field sites, each with a different soil type and indigenous population, or in the laboratory in a sterilized sand, a sterilized peat-vermiculite mixture, or a nonsterile field soil. A mathematical model describing nodulation competitiveness was empirically derived to evaluate the relative competitiveness of the two strains under these conditions. This model relates the proportional representation of the two strains in the inoculum to the proportional representation of nodules occupied by each strain or both strains and provides a measure of competitiveness, which is referred to as the competitiveness index. Statistical comparisons of competitiveness indices showed that the relative competitiveness of KIM5s and CE3 remained constant when the two strains were applied in a constant ratio over a range of inoculum concentrations, from 10(3) to 10(7) cells per seed, and when they were applied in various ratios to six P. vulgaris cultivars. Furthermore, the relative competitiveness of KIM5s and CE3 in the laboratory did not differ significantly from their relative competitiveness at the three field sites studied. Thus, a study of the basis for nodulation competitiveness of KIM5s and CE3 in the laboratory has the potential to provide an understanding of competitiveness both in the laboratory and in the field. PMID:2624457

  20. A second exopolysaccharide of Rhizobium meliloti strain SU47 that can function in root nodule invasion.

    PubMed Central

    Zhan, H J; Levery, S B; Lee, C C; Leigh, J A

    1989-01-01

    Rhizobium meliloti strain SU47 produces the calcofluor-binding exopolysaccharide, succinoglycan, that is required for alfalfa root nodule invasion. Strains derived from R. meliloti SU47 secreted an acidic exopolysaccharide, EPSb, that replaced succinoglycan in nodule invasion. EPSb, which has not formerly been identified among the Rhizobiaceae, consisted of the repeating unit 4,6-O-(1-carboxyethylidene)-alpha-D-Galp1----3(X-O-Ac)-beta-D-G lcp1----3. EPSb synthesis occurred either in strains containing a mutation in a locus designated mucR or in strains with a recombinant cosmid pMuc. mucR mapped slightly counterclockwise from pyr49 on the chromosome, while pMuc contained genes mapping to the megaplasmid pRmeSU47b. In exoA, -F, and -H mutants, which are deficient in normal succinoglycan secretion and nodule invasion, a transposon Tn5 insertion in mucR or the presence of pMuc resulted in EPSb secretion and a restoration of nodule invasion on Medicago sativa and Melilotus alba. Mutants in exoB and exoC were incapable of succinoglycan and EPSb secretion as well as nodule invasion. A mutant that secreted succinoglycan but was incapable of EPSb secretion invaded nodules normally. PMID:2717610

  1. Bacteriocin-Like Substances Produced by Rhizobium japonicum and Other Slow-Growing Rhizobia †

    PubMed Central

    Gross, D. C.; Vidaver, A. K.

    1978-01-01

    Bacteriocin-like substances were commonly produced by slow-growing Rhizobium japonicum and cowpea rhizobia on an L-arabinose medium. Antagonism between strains of R. japonicum was not detected in vitro; however, such strains were often sensitive to some bacteriocins produced by cowpea rhizobia. Inhibitory zones (2 to 8 mm from colony margins), produced by 58 of 66 R. japonicum test strains, were reproducibly detected with Corynebacterium nebraskense as an indicator. Quantitative production was not related to symbiotic properties of effective strains, since nine noninfective strains and one ineffective strain produced bacteriocin. Eight R. japonicum strains that did not produce bacteriocin nevertheless formed effective nodules on soybeans. R. japonicum strains that produced bacteriocin in vitro had no antagonistic effect on nonproducer strains during soybean nodulation. Under controlled conditions, a nonproducer (3I1b135) predominated over a bacteriocin producer (3I1b6) when inoculated at 1:1 and 1:9 ratios. Depending on the particular ratio, up to 38% of the total nodules formed were infected with mixed combinations. The bacteriocin(s) had a restricted host range and antibiotic-like properties which included the ability to be dialyzed and resistance to heat (75 to 80°C, 30 min), Pronase, proteinase K, trypsin, ribonuclease, and deoxyribonuclease. R. japonicum strains representing genetic, serological, cultural, and geographic diversity were differentiated into three groups on the basis of bacteriocin production. Images PMID:570016

  2. Transformation of pWWO in Rhizobium leguminosarum DPT to Engineer Toluene Degrading Ability for Rhizoremediation.

    PubMed

    Goel, Garima; Pandey, Piyush; Sood, Anchal; Bisht, Sandeep; Maheshwari, D K; Sharma, G D

    2012-06-01

    Rhizoremediation of organic xenobiotics is based on interactions between plants and their associated micro-organisms. The present work was designed to engineer a bacterial system having toluene degradation ability along with plant growth promoting characteristics for effective rhizoremediation. pWWO harboring the genes responsible for toluene breakdown was isolated from Pseudomonas putida MTCC 979 and successfully transformed in Rhizobium DPT. This resulted in a bacterial strain (DPT(T)) which had the ability to degrade toluene as well as enhance growth of host plant. The frequency of transformation was recorded 5.7 × 10(-6). DPT produced IAA, siderophore, chitinase, HCN, ACC deaminase, solubilized inorganic phosphate, fixed atmospheric nitrogen and inhibited the growth of Fusarium oxysporum and Macrophomina phaseolina in vitro. During pot assay, 50 ppm toluene in soil was found to inhibit the germination of Cajanus cajan seeds. However when the seeds bacterized with toluene degrading P. putida or R. leguminosarum DPT were sown in pots, again no germination was observed. Non-bacterized as well as bacterized seeds germinated successfully in toluene free soil as control. The results forced for an alternative mode of application of bacteria for rhizoremediation purpose. Hence bacterial suspension was mixed with soil having 50 ppm of toluene. Germination index in DPT treated soil was 100% while in P. putida it was 50%. Untreated soil with toluene restricted the seeds to germinate. PMID:23729882

  3. Regulation of glutamine synthetase II activity in Rhizobium meliloti 104A14.

    PubMed Central

    Shatters, R G; Somerville, J E; Kahn, M L

    1989-01-01

    Most rhizobia contain two glutamine synthetase (GS) enzymes: GSI, encoded by glnA, and GSII, encoded by glnII. We have found that WSU414, a Rhizobium meliloti 104A14 glutamine auxotroph derived from a glnA parental strain, is an ntrA mutant. The R. meliloti glnII promoter region contains DNA sequences similar to those found in front of other genes that require ntrA for their transcription. No GSII was found in the glnA ntrA mutant, and when a translational fusion of glnII to the Escherichia coli lacZ gene was introduced into WSU414, no beta-galactosidase was expressed. These results indicate that ntrA is required for glnII expression. The ntrA mutation did not prevent the expression of GSI. In free-living culture, the level of GSII and of the glnII-lacZ fusion protein was regulated by altering transcription in response to available nitrogen. No GSII protein was detected in alfalfa, pea, or soybean nodules when anti-GSII-specific antiserum was used. Images PMID:2570059

  4. Versatile properties of an exopolysaccharide R-PS18 produced by Rhizobium sp. PRIM-18.

    PubMed

    Priyanka, P; Arun, A B; Ashwini, P; Rekha, P D

    2015-08-01

    Exopolysaccharides (EPS) produced by bacteria have attracted scientific and industrial attention due to their multifunctional properties and relatively easier production. In this study, an EPS viz., R-PS18 produced by Rhizobium sp. PRIM-18 was characterized and its functional properties were assessed. Cell proliferative and in vitro wound healing activities of the EPS were established using human dermal fibroblast (HDF) cells. The isolate produced 2.1 g L(-1) purified EPS (molecular weight 9.33×10(6) Da) comprising of glucose, galactose, and mannose (6.1:1.8:1). Viscosity of 0.25% solution was 23.4 mPa s (shear rate 75 s(-1)) and it showed pseudoplastic and thixotropic behavior. High emulsification, iron chelation, and superoxide scavenging abilities were also observed. Significant increase in HDF cell proliferation and wound healing in vitro was achieved by R-PS18 treatment. Sulfation of R-PS18 significantly enhanced the cell proliferative and wound healing activities. In conclusion, these findings indicate potential applications of R-PS18. PMID:25933542

  5. The Rhizobium etli opt operon is required for symbiosis and stress resistance.

    PubMed

    Vos, K; Braeken, K; Fauvart, M; Ndayizeye, M; Verhaert, J; Zachurzok, S; Lambrichts, I; Michiels, J

    2007-07-01

    Rhizobium etli is a Gram-negative root-colonizing soil bacterium capable of fixing nitrogen while living in symbiosis with its leguminous host Phaseolus vulgaris. A genome-wide screening for R. etli symbiotic mutants revealed a R. etli operon encoding an oligopeptide ABC-transporter (Opt), two redA homologous genes and one redB gene. Expression analysis showed this opt operon to be transcribed both under free-living and symbiotic conditions and expression levels were demonstrated to be growth-phase-dependent. Plants nodulated by R. etli opt mutants showed a reduced symbiotic nitrogen fixation activity (approximately 50% reduction). Growth experiments with opt mutants in the presence of oligopeptides as the sole nitrogen source confirmed the involvement of the opt genes in oligopeptide uptake. Further phenotypic analysis of the opt mutants revealed them to display an enhanced resistance to the oligopeptide antibiotic bacitracin, an increased susceptibility to the beta-lactam antibiotic ampicillin and a decreased osmotolerance. In conclusion, our results demonstrate that the opt operon plays a crucial role during symbiosis and stress resistance. PMID:17564602

  6. Influence of soil variables on in situ plasmid transfer from Escherichia coli to Rhizobium fredii.

    PubMed Central

    Richaume, A; Angle, J S; Sadowsky, M J

    1989-01-01

    A model system was established to determine whether intergeneric plasmid transfer occurs in soil and how various soil variables affect the rate of plasmid transfer. The donor bacterium, Escherichia coli HB101 carrying plasmid pBLK1-2 (pRK2073::Tn5), and the recipient bacterium, Rhizobium fredii USDA 201, were inoculated into a sterile Adelphia fine-sandy-loam soil. Transconjugants were enumerated by direct plating on antibiotic-amended HM [N-2-hydroxyethylpiperazine-N'-2-ethanesulfonic acid; 2-(N-morpholino) ethanesulfonic acid] salts medium. Randomly chosen transconjugants were verified by serological typing and Southern hybridization with a Tn5 gene probe. The maximum transfer frequency was observed after 5 days of incubation (1.8 x 10(-4) per recipient). The influences of clay (0 to 50% addition), organic matter (0 to 15% addition), soil pH (4.3 to 7.25), soil moisture (2 to 40%), and soil incubation temperature (5 to 40 degrees C) on plasmid transfer were examined. Maximum transfer frequencies were noted at a clay addition of 15%, an organic matter addition of 5%, a soil pH of 7.25, a soil moisture content of 8%, and a soil incubation temperature of 28 degrees C. These results indicate that intergeneric plasmid transfer may occur in soil and that soil variables may significantly affect the rate of transfer. Images PMID:2669634

  7. Rearrangement of Actin Microfilaments in Plant Root Hairs Responding to Rhizobium etli Nodulation Signals1

    PubMed Central

    Cárdenas, Luis; Vidali, Luis; Domínguez, Jimena; Pérez, Héctor; Sánchez, Federico; Hepler, Peter K.; Quinto, Carmen

    1998-01-01

    The response of the actin cytoskeleton to nodulation (Nod) factors secreted by Rhizobium etli has been studied in living root hairs of bean (Phaseolus vulgaris) that were microinjected with fluorescein isothiocyanate-phalloidin. In untreated control cells or cells treated with the inactive chitin oligomer, the actin cytoskeleton was organized into long bundles that were oriented parallel to the long axis of the root hair and extended into the apical zone. Upon exposure to R. etli Nod factors, the filamentous actin became fragmented, as indicated by the appearance of prominent masses of diffuse fluorescence in the apical region of the root hair. These changes in the actin cytoskeleton were rapid, observed as soon as 5 to 10 min after application of the Nod factors. It was interesting that the filamentous actin partially recovered in the continued presence of the Nod factor: by 1 h, long bundles had reformed. However, these cells still contained a significant amount of diffuse fluorescence in the apical zone and in the nuclear area, presumably indicating the presence of short actin filaments. These results indicate that Nod factors alter the organization of actin microfilaments in root hair cells, and this could be a prelude for the formation of infection threads. PMID:9501120

  8. Enzymatic Tailoring of Ornithine in the Biosynthesis of the Rhizobium Cyclic Trihydroxamate Siderophore Vicibactin

    PubMed Central

    Heemstra, John R.; Walsh, Christopher T.; Sattely, Elizabeth S.

    2009-01-01

    To acquire iron, the N2-fixing, symbiotic bacterium Rhizobium sp. produce the cyclic tri-hydroxamate siderophore vicibactin, containing a 30-membered tri-lactone scaffold. Herein we report the overproduction and purification of the six proteins VbsACGOLS in the bacterial host Escherichia coli and the reconstitution of the biosynthesis of vicibactin from primary metabolites. The flavoprotein VbsO acts as a pathway-initiating L-ornithine N5-hydroxylase, followed by VbsA which transfers (R)-3-hydroxybutyryl- from the CoA thioester to N5-hydroxyornithine to yield N5-((R)-3-hydroxybutyryl)-N5-hydroxy-L-ornithine. VbsL is a PLP-dependent epimerase acting at C2 of the 10 atom monomer unit. VbsS, a nonribosomal peptide synthetase free standing module, then activates N5-((R)-3-hydroxybutyryl)-N5-hydroxy-D-ornithine as the AMP anhydride on the way to cyclotrimerization to the vicibactin scaffold. The last step, tris-acetylation of the C2 amino group of desacetyl-D-vicibactin to the mature siderophore vicibactin is catalyzed distributively by VbsC, using three molecules of acetyl-CoA. PMID:19778043

  9. Role of motility and chemotaxis in efficiency of nodulation by Rhizobium meliloti. [Medicago sation

    SciTech Connect

    Caetano-Anolles, G.; Wall, L.G.; De Micheli, A.T.; Macchi, E.M.; Bauer, W.D.; Favelukes, G. )

    1988-04-01

    Spontaneous mutants of Rhizobium meliloti L5-30 defective in motility or chemotaxis were isolated and compared against the parent with respect to symbiotic competence. Each of the mutants were able to generate normal nodules on the host plant alfalfa (Medicago sativa), but had slightly delayed nodule formation, diminished nodulation int he initially susceptible region of the host root, and relatively low representation in nodules following co-inoculation with equal numbers of the parent. When inoculated in growth pouches with increasing dosages of the parental strain, the number of nodules formed in the initially susceptible region of the root increased sigmoidally, with an optimum concentration of about 10{sup 5} to 10{sup 6} bacteria/plant. The dose-response behavior of the nonmotile and nonchemotactic mutants was similar, but they required 10- to 30-fold higher concentrations of bacteria to generate the same number of nodules. The distribution frequencies of nodules at different positions along the primary root were very similar for the mutants and parent, indicating that reduced nodulation by the mutants in dose-response experiments probably reflects reduced efficiency of nodule initiation rather than developmentally delayed nodule initiation. The number of bacteria that firmly adsorbed to the host root surface during several hours of incubation was 5- to 20-fold greater for the parent than the mutants.

  10. A Functional Bacterium-to-Plant DNA Transfer Machinery of Rhizobium etli

    PubMed Central

    Lacroix, Benoît; Citovsky, Vitaly

    2016-01-01

    Different strains and species of the soil phytopathogen Agrobacterium possess the ability to transfer and integrate a segment of DNA (T-DNA) into the genome of their eukaryotic hosts, which is mainly mediated by a set of virulence (vir) genes located on the bacterial Ti-plasmid that also contains the T-DNA. To date, Agrobacterium is considered to be unique in its capacity to mediate genetic transformation of eukaryotes. However, close homologs of the vir genes are encoded by the p42a plasmid of Rhizobium etli; this microorganism is related to Agrobacterium, but known only as a symbiotic bacterium that forms nitrogen-fixing nodules in several species of beans. Here, we show that R. etli can mediate functional DNA transfer and stable genetic transformation of plant cells, when provided with a plasmid containing a T-DNA segment. Thus, R. etli represents another bacterial species, besides Agrobacterium, that encodes a protein machinery for DNA transfer to eukaryotic cells and their subsequent genetic modification. PMID:26968003

  11. Rhizobium nod factor signaling. Evidence for a g protein-mediated transduction mechanism

    PubMed Central

    Pingret, JL; Journet, EP; Barker, DG

    1998-01-01

    Rhizobium nodulation (Nod) factors are lipochitooligosaccharide signals that elicit key symbiotic developmental responses in the host legume root. In this study, we have investigated Nod factor signal transduction in the Medicago root epidermis by using a pharmacological approach in conjunction with transgenic plants expressing the Nod factor-responsive reporter construct pMtENOD12-GUS. Evidence for the participation of heterotrimeric G proteins in Nod factor signaling has come from three complementary observations: (1) the amphiphilic peptides mastoparan and Mas7, known G protein agonists, are able to mimic Nod factor-induced epidermal MtENOD12 expression; (2) growth of plants in nodulation-inhibiting conditions (10 mM NH4NO3) leads to a dramatic reduction in both Nod factor- and mastoparan-elicited gene expression; and (3) bacterial pertussis toxin, a well-characterized G protein antagonist, blocks the activities of both the Nod factor and mastoparan. In addition, we have found that antagonists that interfere with phospholipase C activity (neomycin and U73122) and Ca2+ influx/release (EGTA, La3+, and ruthenium red) block Nod factor/mastoparan activity. Taken together, these results are consistent with a Nod factor signal transduction mechanism involving G protein mediation coupled to the activation of both phosphoinositide and Ca2+ second messenger pathways. PMID:9596628

  12. Conjugal Transfer of Megaplasmid 2 between Rhizobium meliloti Strains in Alfalfa Nodules

    PubMed Central

    Pretorius-Güth, Inge-M.; Pühler, Alfred; Simon, Reinhard

    1990-01-01

    A DNA fragment containing the RP4 mob function, as well as the gentamicin and spectinomycin resistance genes, was inserted by gene replacement onto the megaplasmid 2 (pM2) of Rhizobium meliloti 0540 (Inf− EPS−), resulting in PG101 (Inf− EPS−). The self-transfer of pM2 and the mobilization of pM2 by plasmid RP4-4 were investigated during conjugation between PG101 and R. meliloti 2526 (Nod−). In filter conjugations, pM2 was readily mobilized by RP4-4. In addition to this, the self-transfer of one megaplasmid (pM) was detected at a frequency of 3 × 10−7. Bacteria isolated from the nodules of alfalfa and coinoculated with strains PG101 and 2526 showed that pM2 was mobilized at a frequency of approximately 7 × 10−5. Bacterial cell numbers were too low in the nodules for detection of the self-transfer of pM2 to occur. No pM2 transfer was detected in the inoculum. A comparison of the transfer frequencies for the various conjugation conditions revealed that pM2 transfer occurred as frequently in the nodules as in filter conjugations. These results indicate that the nodule creates conditions for gene transfer that are comparable to optimal laboratory conditions. PMID:16348248

  13. Genetics and biochemistry of the Rhizobium meliloti acidic extracellular heteropolysaccharide and its role in nodulation: Annual report for the period 1 June 1986-31 May 1987

    SciTech Connect

    Leigh, J.A.

    1987-01-01

    This document briefly describes studies of the genetics and biochemistry of Rhizobium meliloti exopolysaccharides and their role in alfalfa root nodule formation. Previously the author demonstrated that a large set of mutants (Exo/sup -/) of R. meliloti failed to secrete succinoglycan, an acidic exopolysaccharide of known structure. These mutations belonged to five different loci in the R. meliloti genome. All of the mutants shared the inability to enter alfalfa root nodules, providing strong correlative evidence that succinoglycan is involved in a certain phase in nodule development. In the past year, this research group characterized mutants that were previously designated ''haloless'' mutants. These mutants were thought to be unable to degrade the secreted polysaccharide into diffusible fragments that ordinarily form a halo of binding of a polysaccharide specific dye surrounding a colony of growth. The research team discovered a second acidic exopolysaccharide that is synthesized by certain mutant derivatives of our strain of R. meliloti. This polysaccharide appeared quite distinct from succinoglycan by NMR spectroscopy and appeared to replace succinoglycan in a Tn5-induced mutant called ''halo-clearing'', and in wild type strains containing a certain cosmid from the R. meliloti clone bank. 2 figs.

  14. Differences in Endogenous Levels of Gibberellin-Like Substances in Nodules of Phaseolus lunatus L. Plants Inoculated with Two Rhizobium Strains 1

    PubMed Central

    Evensen, Kathleen B.; Blevins, Dale G.

    1981-01-01

    Lima bean plants (Phaseolus lunatus L.) inoculated with Rhizobium sp. strain 127E14, which lacks constitutive nitrate reductase activity, were significantly taller after 4 weeks of age than plants inoculated with strain 127E15, which contains constitutive nitrate reductase activity. Plants inoculated with either strain responded to application of 5 micrograms gibberellic acid per plant with rapid internode elongation; plants inoculated with strain 127E15 became less responsive to gibberellic acid from 3 to 5 weeks of age, while plants inoculated with strain 127E14 did not. The height of plants inoculated with strain 127E14 was reduced by 20% with application of gibberellin biosynthesis inhibitors to the roots, while height of plants inoculated with strain 127E15 was unaffected. Plants inoculated with strain 127E14 developed nodules containing 4 to 50 times greater quantities of extractable gibberellin-like substances than the nodules of plants inoculated with strain 127E15. Plants inoculated with strain 127E14 had nodules containing larger quantities of gibberellin-like substances in both the acidic and basic ethyl acetate fractions, and these differences were observed before the onset of rapid growth responsible for the difference in plant height. The internode elongation in plants infected with strain 127E14, its reversal by gibberellin biosynthesis inhibitors, and the accumulation of large quantities of gibberellin-like substances in nodules infected with strain 127E14 support the hypothesis that root nodules may contribute gibberellins to the host. PMID:16661869

  15. NopB, a type III secreted protein of Rhizobium sp. strain NGR234, is associated with pilus-like surface appendages.

    PubMed

    Saad, Maged M; Kobayashi, Hajime; Marie, Corinne; Brown, Ian R; Mansfield, John W; Broughton, William J; Deakin, William J

    2005-02-01

    Rhizobium sp. strain NGR234 possesses a functional type three secretion system (TTSS), through which a number of proteins, called nodulation outer proteins (Nops), are delivered to the outside of the cell. A major constraint to the identification of Nops is their low abundance in the supernatants of NGR234 strains grown in culture. To overcome this limitation, a more sensitive proteomics-based strategy was developed. Secreted proteins from wild-type NGR234 were separated by two-dimensional gel electrophoresis, and the gel was compared to similar gels containing the proteins from a TTSS mutant (NGROmegarhcN). To identify the proteins, spots unique to the NGR234 gels were analyzed by matrix-assisted laser desorption ionization-time of flight mass spectrometry and the data were compared to the sequence of the symbiotic plasmid of NGR234. A nonpolar mutant of one of these proteins was generated called NopB. NopB is required for Nop secretion but inhibits the interaction with Pachyrhizus tuberosus and augments nodulation of Tephrosia vogelii. Flavonoids and a functional TTSS are required for the formation of some surface appendages on NGR234. In situ immunogold labeling and isolation of these pili showed that they contain NopB. PMID:15659692

  16. Genomic basis of broad host range and environmental adaptability of Rhizobium tropici CIAT 899 and Rhizobium sp. PRF 81 which are used in inoculants for common bean (Phaseolus vulgaris L.)

    PubMed Central

    2012-01-01

    Background Rhizobium tropici CIAT 899 and Rhizobium sp. PRF 81 are α-Proteobacteria that establish nitrogen-fixing symbioses with a range of legume hosts. These strains are broadly used in commercial inoculants for application to common bean (Phaseolus vulgaris) in South America and Africa. Both strains display intrinsic resistance to several abiotic stressful conditions such as low soil pH and high temperatures, which are common in tropical environments, and to several antimicrobials, including pesticides. The genetic determinants of these interesting characteristics remain largely unknown. Results Genome sequencing revealed that CIAT 899 and PRF 81 share a highly-conserved symbiotic plasmid (pSym) that is present also in Rhizobium leucaenae CFN 299, a rhizobium displaying a similar host range. This pSym seems to have arisen by a co-integration event between two replicons. Remarkably, three distinct nodA genes were found in the pSym, a characteristic that may contribute to the broad host range of these rhizobia. Genes for biosynthesis and modulation of plant-hormone levels were also identified in the pSym. Analysis of genes involved in stress response showed that CIAT 899 and PRF 81 are well equipped to cope with low pH, high temperatures and also with oxidative and osmotic stresses. Interestingly, the genomes of CIAT 899 and PRF 81 had large numbers of genes encoding drug-efflux systems, which may explain their high resistance to antimicrobials. Genome analysis also revealed a wide array of traits that may allow these strains to be successful rhizosphere colonizers, including surface polysaccharides, uptake transporters and catabolic enzymes for nutrients, diverse iron-acquisition systems, cell wall-degrading enzymes, type I and IV pili, and novel T1SS and T5SS secreted adhesins. Conclusions Availability of the complete genome sequences of CIAT 899 and PRF 81 may be exploited in further efforts to understand the interaction of tropical rhizobia with common bean

  17. Phosphoglycerol substituents present on the cyclic beta-1,2-glucans of Rhizobium meliloti 1021 are derived from phosphatidylglycerol.

    PubMed Central

    Miller, K J; Gore, R S; Benesi, A J

    1988-01-01

    The synthesis of periplasmic cyclic beta-1,2-glucans is a property unique to species of the family Rhizobiaceae. For this reason, it is generally believed that these molecules may play an important role in the plant infection process. In the present study, we determined that the cyclic beta-1,2-glucans produced by Rhizobium meliloti 1021 were predominantly anionic in character and contained both phosphoglycerol and succinic acid substituents. In addition, we demonstrated that phosphatidylglycerol was the source of the phosphoglycerol substituents present on these oligosaccharides and that greater than 60% of the total phospholipid turnover in this organism involved this substitution reaction. PMID:3170478

  18. [Effect of cultivation conditions on the accumulation of poly-beta-hydroxy-butyric acid in Rhizobium lupini].

    PubMed

    Yushkova, L A; Fedulova, N G; Romanov, V I; Kretovich, W L

    1975-01-01

    The influence of the age of the culture and nitrogen source on the accumulation of poly-beta-hydroxybutyric acid by different strains of Rhizobium lupini was studied. The accumulation depended on the age of the culture and reached maximum at the end of the logarithmic and at the beginning of the stationary phase of the bacterial growth (about 50-60% dry weight). The accumulation varied in relation to the nitrogen source used: it was the highest in the glutamate medium and the lowest on nitrate nitrogen; the culture grown on ammonium phosphate was intermediate. PMID:1208373

  19. Development and evaluation of multispecies test protocols for assessing chemical toxicity

    SciTech Connect

    Garten, C.T. Jr.; Suter, G.W. II; Blaylock, B.G.

    1985-06-01

    Toxicity testing is a well-recognized tool to assist in evaluating the hazards of chemicals to individual biological species. Multispecies toxicity tests, however, are now well developed. Three test systems were examined: the legume-Rhizobium symbiosis for N-fixation, soil microbial populations, and algal multispecies interactions. Test protocols were to be developed and tested using several different chemicals. Test protocols for the legume-Rhizobium and soil microorganisms systems were developed and are presented. The algal multispecies system will require more research, and thus no protocol was recommended at this time. Separate abstracts were prepared for each test system. (ACR)

  20. Biogeography of Rhizobium radiobacter and distribution of associated temperate phages in deep subseafloor sediments

    PubMed Central

    Engelhardt, Tim; Sahlberg, Monika; Cypionka, Heribert; Engelen, Bert

    2013-01-01

    Bacteriophages might be the main ‘predators' in the marine deep subsurface and probably have a major impact on indigenous microbial communities. To identify their function within this habitat, we have determined their abundance and distribution along the sediment columns of two continental margin and two open ocean sites that were recovered during Leg 201 of the Ocean Drilling Program. For all investigated sites, viral abundance followed the total cell numbers with a virus-to-cell ratio between 1 and 10 in the upper 100 mbsf (meters below seafloor). An increasing ratio of about 20 in deeper layers indicated an ongoing viral production in up to 11 Ma old sediments. We have used Rhizobium radiobacter as the most frequently isolated organism from the deep subsurface with a high in situ abundance to identify the frequency of associated rhizobiophages. In this study, 16S rRNA gene copies of R. radiobacter accounted for up to 5.6% of total bacterial 16S rRNA genes (average: 0.75%) as detected by quantitative PCR. A distinctive distribution was identified for R. radiobacter as indicated by a site-specific arrangement of genetically similar populations. Whole genome information of rhizobiophage RR1-A was used to generate a primer system for quantitative PCR specifically targeting the prophage antirepressor gene, indicative for temperate phages. The quantification of this gene within various sediment horizons showed a contribution of temperate phages of up to 14.3% to the total viral abundance. Thus, the high amount of temperate phages within the sediments and among all investigated isolates indicates that lysogeny is the main viral proliferation mode in deep subsurface populations. PMID:22855213

  1. Cloning and Identification of Conjugative Transfer Origins in the Rhizobium meliloti Genome

    PubMed Central

    Herrera-Cervera, Jose A.; Sanjuan-Pinilla, Julio M.; Olivares, Jose; Sanjuan, Juan

    1998-01-01

    A simple approach was used to identify Rhizobium meliloti DNA regions with the ability to convert a nontransmissible vector into a mobilizable plasmid, i.e., to contain origins of conjugative transfer (oriT, mob). RecA-defective R. meliloti merodiploid populations, where each individual contained a hybrid cosmid from an R. meliloti GR4 gene library, were used as donors en masse in conjugation with another R. meliloti recipient strain, selecting transconjugants for vector-encoded antibiotic resistance. Restriction analysis of cosmids isolated from individual transconjugants resulted in the identification of 11 nonoverlapping DNA regions containing potential oriTs. Individual hybrid cosmids were confirmed to be mobilized from the original recA donors at frequencies ranging from 10−2 to 10−5 per recipient cell. DNA hybridization experiments showed that seven mob DNA regions correspond to plasmid replicons: four on symbiotic megaplasmid 1 (pSym1), one on pSym2, and another two on each of the two cryptic plasmids harbored by R. meliloti GR4. Another three mob clones could not be located to any plasmid and were therefore preliminarily assigned to the chromosome. With this strategy, we were able to characterize the oriT of the conjugative plasmid pRmeGR4a, which confirmed the reliability of the approach to select for oriTs. Moreover, transfer of the 11 mob cosmids from R. meliloti into Escherichia coli occurred at frequencies as high as 10−1, demonstrating the R. meliloti gene transfer capacity is not limited to the family Rhizobiaceae. Our results show that the R. meliloti genome contains multiple oriTs that allow efficient DNA mobilization to rhizobia as well as to phylogenetically distant gram-negative bacteria. PMID:9721299

  2. Roles of Predicted Glycosyltransferases in the Biosynthesis of the Rhizobium etli CE3 O Antigen

    PubMed Central

    Ojeda, Kristylea J.; Simonds, Laurie

    2013-01-01

    The Rhizobium etli CE3 O antigen is a fixed-length heteropolymer. The genetic regions required for its synthesis have been identified, and the nucleotide sequences are known. The structure of the O antigen has been determined, but the roles of specific genes in synthesizing this structure are relatively unclear. Within the known O-antigen genetic clusters of this strain, nine open reading frames (ORFs) were found to contain a conserved glycosyltransferase domain. Each ORF was mutated, and the resulting mutant lipopolysaccharide (LPS) was analyzed. Tricine SDS-PAGE revealed stepwise truncations of the O antigen that were consistent with differences in mutant LPS sugar compositions and reactivity with O-antigen-specific monoclonal antibodies. Based on these results and current theories of O-antigen synthesis, specific roles were deduced for each of the nine glycosyltransferases, and a model for biosynthesis of the R. etli CE3 O antigen was proposed. In this model, O-antigen biosynthesis is initiated with the addition of N-acetyl-quinovosamine-phosphate (QuiNAc-P) to bactoprenol-phosphate by glycosyltransferase WreU. Glycosyltransferases WreG, WreE, WreS, and WreT would each act once to attach mannose, fucose, a second fucose, and 3-O-methyl-6-deoxytalose (3OMe6dTal), respectively. WreH would then catalyze the addition of methyl glucuronate (MeGlcA) to complete the first instance of the O-antigen repeat unit. Four subsequent repeats of this unit composed of fucose, 3OMe6dTal, and MeGlcA would be assembled by a cycle of reactions catalyzed by two additional glycosyltransferases, WreM and WreL, along with WreH. Finally, the O antigen would be capped by attachment of di- or tri-O-methylated fucose as catalyzed by glycosyltransferase WreB. PMID:23435981

  3. Evidence of an American Origin for Symbiosis-Related Genes in Rhizobium lusitanum ▿

    PubMed Central

    Valverde, Angel; Velázquez, Encarna; Cervantes, Emilio; Igual, José M.; van Berkum, Peter

    2011-01-01

    Randomly amplified polymorphic DNA (RAPD) analysis was used to investigate the diversity of 179 bean isolates recovered from six field sites in the Arcos de Valdevez region of northwestern Portugal. The isolates were divided into 6 groups based on the fingerprint patterns that were obtained. Representatives for each group were selected for sequence analysis of 4 chromosomal DNA regions. Five of the groups were placed within Rhizobium lusitanum, and the other group was placed within R. tropici type IIA. Therefore, the collection of Portuguese bean isolates was shown to include the two species R. lusitanum and R. tropici. In plant tests, the strains P1-7, P1-1, P1-2, and P1-16 of R. lusitanum nodulated and formed nitrogen-fixing symbioses both with Phaseolus vulgaris and Leucaena leucocephala. A methyltransferase-encoding nodS gene identical with the R. tropici locus that confers wide host range was detected in the strain P1-7 as well as 24 others identified as R. lusitanum. A methyltransferase-encoding nodS gene also was detected in the remaining isolates of R. lusitanum, but in this case the locus was that identified with the narrow-host-range R. etli. Representatives of isolates with the nodS of R. etli formed effective nitrogen-fixing symbioses with P. vulgaris and did not nodulate L. leucocephala. From sequence data of nodS, the R. lusitanum genes for symbiosis were placed within those of either R. tropici or R. etli. These results would support the suggestion that R. lusitanum was the recipient of the genes for symbiosis with beans from both R. tropici and R. etli. PMID:21705533

  4. Identification of protein secretion systems and novel secreted proteins in Rhizobium leguminosarum bv. viciae

    PubMed Central

    Krehenbrink, Martin; Downie, J Allan

    2008-01-01

    Background Proteins secreted by bacteria play an important role in infection of eukaryotic hosts. Rhizobia infect the roots of leguminous plants and establish a mutually beneficial symbiosis. Proteins secreted during the infection process by some rhizobial strains can influence infection and modify the plant defence signalling pathways. The aim of this study was to systematically analyse protein secretion in the recently sequenced strain Rhizobium leguminosarum bv. viciae 3841. Results Similarity searches using defined protein secretion systems from other Gram-negative bacteria as query sequences revealed that R. l. bv. viciae 3841 has ten putative protein secretion systems. These are the general export pathway (GEP), a twin-arginine translocase (TAT) secretion system, four separate Type I systems, one putative Type IV system and three Type V autotransporters. Mutations in genes encoding each of these (except the GEP) were generated, but only mutations affecting the PrsDE (Type I) and TAT systems were observed to affect the growth phenotype and the profile of proteins in the culture supernatant. Bioinformatic analysis and mass fingerprinting of tryptic fragments of culture supernatant proteins identified 14 putative Type I substrates, 12 of which are secreted via the PrsDE, secretion system. The TAT mutant was defective for the symbiosis, forming nodules incapable of nitrogen fixation. Conclusion None of the R. l. bv. viciae 3841 protein secretion systems putatively involved in the secretion of proteins to the extracellular space (Type I, Type IV, Type V) is required for establishing the symbiosis with legumes. The PrsDE (Type I) system was shown to be the major route of protein secretion in non-symbiotic cells and to secrete proteins of widely varied size and predicted function. This is in contrast to many Type I systems from other bacteria, which typically secrete specific substrates encoded by genes often localised in close proximity to the genes encoding the

  5. Evidence of an American origin for symbiosis-related genes in Rhizobium lusitanum.

    PubMed

    Valverde, Angel; Velázquez, Encarna; Cervantes, Emilio; Igual, José M; van Berkum, Peter

    2011-08-15

    Randomly amplified polymorphic DNA (RAPD) analysis was used to investigate the diversity of 179 bean isolates recovered from six field sites in the Arcos de Valdevez region of northwestern Portugal. The isolates were divided into 6 groups based on the fingerprint patterns that were obtained. Representatives for each group were selected for sequence analysis of 4 chromosomal DNA regions. Five of the groups were placed within Rhizobium lusitanum, and the other group was placed within R. tropici type IIA. Therefore, the collection of Portuguese bean isolates was shown to include the two species R. lusitanum and R. tropici. In plant tests, the strains P1-7, P1-1, P1-2, and P1-16 of R. lusitanum nodulated and formed nitrogen-fixing symbioses both with Phaseolus vulgaris and Leucaena leucocephala. A methyltransferase-encoding nodS gene identical with the R. tropici locus that confers wide host range was detected in the strain P1-7 as well as 24 others identified as R. lusitanum. A methyltransferase-encoding nodS gene also was detected in the remaining isolates of R. lusitanum, but in this case the locus was that identified with the narrow-host-range R. etli. Representatives of isolates with the nodS of R. etli formed effective nitrogen-fixing symbioses with P. vulgaris and did not nodulate L. leucocephala. From sequence data of nodS, the R. lusitanum genes for symbiosis were placed within those of either R. tropici or R. etli. These results would support the suggestion that R. lusitanum was the recipient of the genes for symbiosis with beans from both R. tropici and R. etli. PMID:21705533

  6. The Rhizobium meliloti rhizopine mos locus is a mosaic structure facilitating its symbiotic regulation.

    PubMed Central

    Murphy, P J; Trenz, S P; Grzemski, W; De Bruijn, F J; Schell, J

    1993-01-01

    The Rhizobium meliloti L5-30 mos locus, encoding biosynthesis of the rhizopine 3-O-methyl-scyllo-inosamine, is shown to be a mosaic structure. The mos locus consists of four open reading frames (ORFs) (ORF1 and mosABC) arranged in an operon structure. Within this locus, several domains of homology with other prokaryotic symbiotic genes (nifH, fixA, fixU, and nifT) are present, suggesting that this locus may represent a hot spot for rearrangement of symbiotic genes. Unusually, these domains are present in the coding as well as noncoding regions of the mos locus. Proteins corresponding to those encoded by mosABC, but not ORF1, have been detected in nodule extracts by using antibodies. As ORF1 shows extensive homology with the 5' region of the nifH gene (P.J. Murphy, N. Heycke, S.P. Trenz, P. Ratet, F.J. de Bruijn, and J. Schell, Proc. Natl. Acad. Sci. USA 85:9133-9137, 1988) and a frameshift mutation indicates that expression of this ORF is not required for mos activity, we propose that the mos locus has acquired a duplicated copy of nifH, including the promoter region, in order to become symbiotically regulated. Surprisingly, since the functions are likely different, MosA has an amino acid sequence similar to that of the DapA protein of Escherichia coli. The central domain of MosB has extensive homology with a range of diverse proteins involved with carbohydrate metabolism in either antibiotic or outer-cell-wall biosynthesis. This region is also common to the regulatory proteins DegT and DnrJ, suggesting a regulatory role for MosB. The structure of MosC is consistent with its being a membrane transport protein. Images PMID:8349559

  7. Expression Cloning of Three Rhizobium leguminosarum Lipopolysaccharide Core Galacturonosyltransferases*◻

    PubMed Central

    Kanjilal-Kolar, Suparna; Basu, Shib Sankar; Kanipes, Margaret I.; Guan, Ziqiang; Garrett, Teresa A.; Raetz, Christian R. H.

    2009-01-01

    The lipid A and core regions of the lipopolysaccharide in Rhizobium leguminosarum, a nitrogen-fixing plant endosymbiont, are strikingly different from those of Escherichia coli. In R. leguminosarum lipopolysaccharide, the inner core is modified with three galacturonic acid (GalA) moieties, two on the distal 3-deoxy-D-manno-octulosonic acid (Kdo) unit and one on the mannose residue. Here we describe the expression cloning of three novel GalA transferases from a 22-kb R. leguminosarum genomic DNA insert-containing cosmid (pSGAT). Two of these enzymes modify the substrate, Kdo2-[4′-32P]lipid IVA and its 1-dephosphorylated derivative on the distal Kdo residue, as indicated by mild acid hydrolysis. The third enzyme modifies the mannose unit of the substrate mannosyl-Kdo2-1-dephospho-[4′-32P]lipid IVA. Sequencing of a 7-kb subclone derived from pSGAT revealed three putative membrane-bound glycosyltransferases, now designated RgtA, RgtB, and RgtC. Transfer by tri-parental mating of these genes into Sinorhizobium meliloti 1021, a strain that lacks these particular GalA residues, results in the heterologous expression of the GalA transferase activities seen in membranes of cells expressing pSGAT. Reconstitution experiments with the individual genes demonstrated that the activity of RgtA precedes and is necessary for the subsequent activity of RgtB, which is followed by the activity of RgtC. Electrospray ionization-tandem mass spectrometry and gas-liquid chromatography of the product generated in vitro by RgtA confirmed the presence of a GalA moiety. No in vitro activity was detected when RgtA was expressed in Escherichia coli unless Rhizobiaceae membranes were also included. PMID:16497674

  8. Dodecaprenyl Phosphate-Galacturonic Acid as a Donor Substrate for Lipopolysaccharide Core Glycosylation in Rhizobium leguminosarum*

    PubMed Central

    Kanjilal-Kolar, Suparna; Raetz, Christian R. H.

    2008-01-01

    The lipid A and inner core regions of Rhizobium leguminosarum lipopolysaccharide contain four galacturonic acid (GalA) residues. Two are attached to the outer unit of the 3-deoxy-D-manno-octulosonic acid (Kdo) disaccharide, one to the mannose residue, and one to the 4′-position of lipid A. The enzymes RgtA and RgtB, described in the accompanying article, catalyze GalA transfer to the Kdo residue, whereas RgtC is responsible for modification of the core mannose unit. Heterologous expression of RgtA in Sinorhizhobium meliloti 1021, a strain that normally lacks GalA modifications on its Kdo disaccharide, resulted in detectable GalA transferase activity in isolated membrane preparations, suggesting that the appropriate GalA donor substrate is available in S. meliloti membranes. In contrast, heterologous expression of RgtA in Escherichia coli yielded inactive membranes. However, RgtA activity was detectable in the E. coli system when total lipids from R. leguminosarum 3841 or S. meliloti 1021 were added. We have now purified and characterized dodecaprenyl (C60) phosphate-GalA as a minor novel lipid of R. leguminosarum 3841 and S. meliloti. This substance is stable to mild base hydrolysis and was purified by DEAE-cellulose column chromatography. Its structure was established by a combination of electrospray ionization mass spectrometry and gas-liquid chromatography. Purified dodecaprenyl phosphate-GalA supports the efficient transfer of GalA to Kdo2-1-dephospho-lipid IVA by membranes of E. coli cells expressing RgtA, RgtB, and RgtC. The identification of a polyisoprene phosphate-GalA donor substrate suggests that the active site of RgtA faces the periplasmic side of the inner membrane. This work represents the first definitive characterization of a lipid-linked GalA derivative with the proposed structure dodecaprenyl phosphate-β-D-GalA. PMID:16497671

  9. Rhizavidin from Rhizobium etli: the first natural dimer in the avidin protein family

    PubMed Central

    Helppolainen, Satu H.; Nurminen, Kirsi P.; Määttä, Juha A. E.; Halling, Katrin K.; Slotte, J. Peter; Huhtala, Tuulia; Liimatainen, Timo; Ylä-Herttuala, Seppo; Airenne, Kari J.; Närvänen, Ale; Jänis, Janne; Vainiotalo, Pirjo; Valjakka, Jarkko; Kulomaa, Markku S.; Nordlund, Henri R.

    2007-01-01

    Rhizobium etli CFN42 is a symbiotic nitrogen-fixing bacterium of the common bean Phaseolus vulgaris. The symbiotic plasmid p42d of R. etli comprises a gene encoding a putative (strept)avidin-like protein, named rhizavidin. The amino acid sequence identity of rhizavidin in relation to other known avidin-like proteins is 20–30%. The amino acid residues involved in the (strept)avidin–biotin interaction are well conserved in rhizavidin. The structural and functional properties of rhizavidin were carefully studied, and we found that rhizavidin shares characteristics with bradavidin, streptavidin and avidin. However, we found that it is the first naturally occurring dimeric protein in the avidin protein family, in contrast with tetrameric (strept)avidin and bradavidin. Moreover, it possesses a proline residue after a flexible loop (GGSG) in a position close to Trp-110 in avidin, which is an important biotin-binding residue. [3H]Biotin dissociation and ITC (isothermal titration calorimetry) experiments showed dimeric rhizavidin to be a high-affinity biotin-binding protein. Its thermal stability was lower than that of avidin; although similar to streptavidin, it was insensitive to proteinase K. The immunological cross-reactivity of rhizavidin was tested with human serum samples obtained from cancer patients exposed to (strept)avidin. No significant cross-reactivity was observed. The biodistribution of the protein was studied by SPECT (single-photon emission computed tomography) imaging in rats. Similarly to avidin, rhizavidin was observed to accumulate rapidly, mainly in the liver. Evidently, rhizavidin could be used as a complement to (strept)avidin in (strept)avidin–biotin technology. PMID:17447892

  10. Fermentable non-starch polysaccharides increases the abundance of Bacteroides-Prevotella-Porphyromonas in ileal microbial community of growing pigs.

    PubMed

    Ivarsson, E; Roos, S; Liu, H Y; Lindberg, J E

    2014-11-01

    Most plant-origin fiber sources used in pig production contains a mixture of soluble and insoluble non-starch polysaccharides (NSP). The knowledge about effects of these sources of NSP on the gut microbiota and its fermentation products is still scarce. The aim of this study was to investigate effects of feeding diets with native sources of NSP on the ileal and fecal microbial composition and the dietary impact on the concentration of short-chain fatty acids (SCFA) and lactic acid. The experiment comprised four diets and four periods in a change-over design with seven post valve t-cecum cannulated growing pigs. The four diets were balanced to be similar in NSP content and included one of four fiber sources, two diets were rich in pectins, through inclusion of chicory forage (CFO) and sugar beet pulp, and two were rich in arabinoxylan, through inclusion of wheat bran (WB) and grass meal. The gut microbial composition was assessed with terminal restriction fragment (TRF) length polymorphism and the abundance of Lactobacillus spp., Enterobacteriaceae, Bacteroides-Prevotella-Porphyromonas and the β-xylosidase gene, xynB, were assessed with quantitative PCR. The gut microbiota did not cluster based on NSP structure (arabinoxylan or pectin) rather, the effect was to a high degree ingredient specific. In pigs fed diet CFO, three TRFs related to Prevotellaceae together consisted of more than 25% of the fecal microbiota, which is about 3 to 23 times higher (P<0.05) than in pigs fed the other diets. Whereas pigs fed diet WB had about 2 to 22 times higher abundance (P<0.05) of Megasphaera elsdenii in feces and about six times higher abundance (P<0.05) of Lactobacillus reuteri in ileal digesta than pigs fed the other diets. The total amount of digested NSP (r=0.57; P=0.002), xylose (r=0.53; P=0.004) and dietary fiber (r=0.60; P=0.001) in ileal digesta were positively correlated with an increased abundance of Bacteroides-Prevotella-Porphyromonas. The effect on SCFA was

  11. Distribution and Abundance of Human Specific Bacteroides and Relation to Traditional Indicators in an Urban Tropical Catchment

    NASA Astrophysics Data System (ADS)

    Nshimyimana, J.; Shanahan, P.; Thompson, J. R.; Ekklesia, E.; Chua Hock Chye, L.

    2012-12-01

    The Singapore government through its Public Utilities Board is interested in opening Kranji Reservoir to recreational use. However, water courses within the Kranji Reservoir catchment contain human fecal indicator bacteria above recreational water quality criteria; their sources and distribution are unknown. The primary goals of this study were to determine the distribution of fecal indicator bacteria in drainages and water bodies in the Kranji reservoir catchment area. Total coliforms, E. coli, and the DNA-based HF marker (targeting a human specific strain of Bacteroides) were quantified in 27 samples collected in January 2009 and 54 samples collected in July 2009. Correlation of HF marker cell equivalents (CE) and E. coli abundance (colony forming units (CFU) or Most Probable Number (MPN)) to different land-use categories revealed potential sources of fecal contamination to the Kranji reservoir. Notably, areas designated as farming/agricultural were associated with the highest levels of E. coli (geometric mean 30,500 CFU/100 ml) and HF marker (1.23±1.13x106 CE/100 ml ± S.D.) while in general lower HF marker and E. coli levels were observed in residential areas, undeveloped areas, and within the Kranji reservoir (i.e. Kranji Reservoir had 2 to 17 MPN/100 ml of E. coli and 103 to 105 HF marker CE/100 ml). A partial survey of potential point sources for fecal contamination within the farming area revealed a wastewater effluent stream with HF marker levels exceeding 107 CE/100ml. As observed in previous studies, total coliforms and E. coli levels were weakly (R<0.4), or anti- correlated to HF marker concentrations across different land uses. Weak correspondence between traditional indicators (E. coli, total coliforms) and molecular indicators (HF marker) may be explained by differences in the ability of the respective organisms to grow or survive under aerated tropical conditions. The HF marker sequence matches that of Bacteroides dorei, an obligate anaerobe that

  12. Bifidobacterium, Bacteroides, and Clostridium spp. in fecal samples from breast-fed and bottle-fed infants with and without iron supplement.

    PubMed Central

    Mevissen-Verhage, E A; Marcelis, J H; de Vos, M N; Harmsen-van Amerongen, W C; Verhoef, J

    1987-01-01

    Bifidobacterium, Bacteroides, and Clostridium spp. isolated from the feces of 23 neonates during the first 3 months of life were identified. Of the 23 neonates, 10 were breast fed, 6 received an infant formula with iron supplement (5 mg/liter), and 7 received the formula without iron supplement (iron concentration, less than 0.5 mg/liter). The Bifidobacterium spp. most frequently isolated from the three groups of infants were B. longum, B. breve, B. adolescentis, and B. bifidum. The bacteroides spp. most frequently isolated were B. fragilis and B. vulgatus. The most common Clostridium sp. in the three groups of infants was C. perfringens. The type of milk did not select for species of Bifidobacterium, Bacteroides, or Clostridium, except for Clostridium butyricum, which was isolated significantly more often from bottle-fed infants with iron supplement than from the other groups, and Clostridium tertium, which was more often isolated from breast-fed infants. The species of the three anaerobic genera did not persist for a long period of time in the three groups of infants. PMID:3818925

  13. The structure and molecular mechanics calculations of the cyclic (1 → 2)-β- D-glucan secreted by Rhizobium tropici CIAT 899

    NASA Astrophysics Data System (ADS)

    Gil Serrano, Antonio M.; Franco-Rodríguez, Guillermo; González-Jiménez, Isabel; Tejero-Mateo, Pilar; Molina, José Molina; Dobado, J. A.; Megías, Manuel; Romero, Maria Jesús

    1993-12-01

    The structure of the extracellular cyclic (1 → 2)-β- D-glucan secreted by Rhizobium tropici CIAT 899 has been studied by methylation analysis, 1D and 2D NMR experiments, HPLC and FAB-MS. Molecular mechanics (MM2) and theoretical 3JHH coupling constants calculations were performed.

  14. Ensifer, Phyllobacterium and Rhizobium species occupy nodules of Medicago sativa (alfalfa) and Melilotus alba (sweet clover) grown at a Canadian site without a history of cultivation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phage resistant and susceptible bacteria from nodules of alfalfa and sweet clover grown at a site without a known history of cultivation, were identified as Ensifer, Rhizobium and Phyllobacterium species based on sequence analysis of ribosomal (16S and 23S rRNA)and protein encoding (atpD and recA) g...

  15. The exopolysaccharide of Rhizobium sp. YAS34 is not necessary for biofilm formation on Arabidopsis thaliana and Brassica napus roots but contributes to root colonization

    PubMed Central

    Santaella, Catherine; Schue, Mathieu; Berge, Odile; Heulin, Thierry; Achouak, Wafa

    2008-01-01

    Microbial exopolysaccharides (EPSs) play key roles in plant–microbe interactions, such as biofilm formation on plant roots and legume nodulation by rhizobia. Here, we focused on the function of an EPS produced by Rhizobium sp. YAS34 in the colonization and biofilm formation on non-legume plant roots (Arabidopsis thaliana and Brassica napus). Using random transposon mutagenesis, we isolated an EPS-deficient mutant of strain YAS34 impaired in a glycosyltransferase gene (gta). Wild type and mutant strains were tagged with a plasmid-born GFP and, for the first time, the EPS produced by the wild-type strain was seen in the rhizosphere using selective carbohydrate probing with a fluorescent lectin and confocal laser-scanning microscopy. We show for the fist time that Rhizobium forms biofilms on roots of non-legumes, independently of the EPS synthesis. When produced by strain YAS34 wild type, EPS is targeted at specific parts of the plant root system. Nutrient fluctuations, root exudates and bacterial growth phase can account for such a production pattern. The EPS synthesis in Rhizobium sp. YAS34 is not essential for biofilm formation on roots, but is critical to colonization of the basal part of the root system and increasing the stability of root-adhering soil. Thus, in Rhizobium sp. YAS34 and non-legume interactions, microbial EPS is implicated in root–soil interface, root colonization, but not in biofilm formation. PMID:18507672

  16. Lipid A biosynthesis in Rhizobium leguminosarum: Role of a 2-keto-3-deoxyoctulosonate-activated 4{prime} phosphatase

    SciTech Connect

    Price, N.P.J.; Jeyaretnam, B.; Carlson, R.W.

    1995-08-01

    Lipid A from several strains of the N{sub 2}-fixing bacterium Rhizobium leguminosarum displays significant structural differences from Escherichia coli lipid A, one of which is the complete absence of phosphate groups. However, the first seven enzymes of E. coli lipid A biosynthesis, leading from UDP-GlcNAc to the phosphorylated intermediate, 2-keto-3-deoxyoctulosonate (Kdo{sub 2})-lipid IV{sub A}, are present in R. leguminosarum. We now describe a membrane-bound phosphatase in R. leguminosarum extracts that removes the 4{prime} phosphate of Kdo{sub 2}-lipid IV{sub A}. The 4{prime} phosphatase is selective for substrates containing the Kdo domain. It is present in extracts of R. leguminosarum biovars phaseoli, viciae, and trifolii but is not detectable in E. coli and Rhizobium meliloti. A nodulation-defective strain (24AR) of R. leguminosarum bovar trifolii, known to contain a 4{prime} phosphate residue on its lipid A, also lacks measurable 4{prime} phosphatase activity. the Kdo-dependent 4{prime} phosphatase appears to be a key reaction in a pathway for generating phosphate-deficient lipid A.

  17. Evaluation of microbial populations, Rhizobium Trifolii, and endomycorrhizal associations in reclamation of surface mine spoils in Texas

    SciTech Connect

    Mott, J.B.

    1984-01-01

    The deficiency of nitrogen and phosphorus in mixed overburden mine spoils has resulted in interest in strategies to minimize fertilizer application. In this study, the abundance of microbial populations, with emphasis on those involved in nitrogen cycle transformations was estimated in variously aged spoils. Two beneficial plant-microbe associations, the clover-Rhizobium trifolii symbiosis and endomycorrhizal associations, were investigated in field and laboratory studies. While most groups of microorganisms regained pre-mining levels in revegetated spoils within 1.5 years after disturbance, algal populations were still reduced ten years after mining. Populations of nitrifying bacteria and asymbiotic nitrogen-fixing bacteria were as high in all spoils as in unmined soil. Indigenous populations of ineffective R. trifolii were present in spoil banks and older revegetated spoil. A laboratory study of survival of three commercial strains of R. trifolii for subterranean clover showed lethal effects of high temperature (45/sup 0/C) especially in moist spoil, and superior survival of strain 162X95. Endomycorrhizal associations, evaluated by assessment of root infection in bermudagrass, reached pre-mining levels by three to seven years after disturbance. Growth chamber studies to investigate the effects of the two symbiotic associations on subterranean clover in mine spoil at different fertility levels indicated that dual infection with Rhizobium and VAM fungi was most beneficial for plant growth, nitrogen fixation, and nitrogen and phosphorus contents.

  18. Characterization and symbiotic importance of acidic extracellular polysaccharides of Rhizobium sp. strain GRH2 isolated from acacia nodules.

    PubMed Central

    Lopez-Lara, I M; Orgambide, G; Dazzo, F B; Olivares, J; Toro, N

    1993-01-01

    Rhizobium sp. wild-type strain GRH2 was originally isolated from root nodules of the leguminous tree Acacia cyanophylla and has a broad host range which includes herbaceous legumes, e.g., Trifolium spp. We examined the extracellular exopolysaccharides (EPSs) produced by strain GRH2 and found three independent glycosidic structures: a high-molecular-weight acidic heteropolysaccharide which is very similar to the acidic EPS produced by Rhizobium leguminosarum biovar trifolii ANU843, a low-molecular-weight native heterooligosaccharide resembling a dimer of the repeat unit of the high-molecular-weight EPS, and low-molecular-weight neutral beta (1,2)-glucans. A Tn5 insertion mutant derivative of GRH2 (exo-57) that fails to form acidic heteropolysaccharides was obtained. This Exo- mutant formed nitrogen-fixing nodules on Acacia plants but infected a smaller proportion of cells in the central zone of the nodules than did wild-type GRH2. In addition, the exo-57 mutant failed to nodulate several herbaceous legume hosts that are nodulated by wild-type strain GRH2. Images PMID:8491702

  19. Monocolonization of germ-free mice with Bacteroides fragilis protects against dextran sulfate sodium-induced acute colitis.

    PubMed

    Chiu, Chien-Chao; Ching, Yung-Hao; Wang, Yu-Chih; Liu, Ju-Yun; Li, Yen-Peng; Huang, Yen-Te; Chuang, Hsiao-Li

    2014-01-01

    Ulcerative colitis is inflammatory conditions of the colon caused by interplay of genetic and environmental factors. Previous studies indicated that the gut microflora may be involved in the colonic inflammation. Bacteroides fragilis (BF) is a Gram-negative anaerobe belonging to the colonic symbiotic. We aimed to investigate the protective role of BF in a colitis model induced in germ-free (GF) mice by dextran sulfate sodium (DSS). GF C57BL/6JNarl mice were colonized with BF for 28 days before acute colitis was induced by DSS. BF colonization significantly increased animal survival by 40%, with less reduction in colon length, and decreased infiltration of inflammatory cells (macrophages and neutrophils) in colon mucosa following challenge with DSS. In addition, BF could enhance the mRNA expression of anti-inflammatory-related cytokine such as interleukin 10 (IL-10) with polymorphism cytokine IL-17 and diminish that of proinflammatory-related tumor necrosis factor α with inducible nitric oxide synthase in the ulcerated colon. Myeloperoxidase activity was also decreased in BF-DSS mice. Taking these together, the BF colonization significantly ameliorated DSS-induced colitis by suppressing the activity of inflammatory-related molecules and inducing the production of anti-inflammatory cytokines. BF may play an important role in maintaining intestinal immune system homeostasis and regulate inflammatory responses. PMID:24971344

  20. Effect of distance from the polluting focus on relative concentrations of Bacteroides fragilis phages and coliphages in mussels.

    PubMed Central

    Lucena, F; Lasobras, J; McIntosh, D; Forcadell, M; Jofre, J

    1994-01-01

    Concentrations of fecal bacteria, somatic and F-specific coliphages, and phages infecting Bacteroides fragilis in naturally occurring black mussels (Mytilus edulis) were determined. Mussels were collected over a 7-month period at four sampling sites with different levels of fecal pollution. Concentrations of both fecal bacteria and bacteriophages in mussel meat paralleled the concentration of fecal bacteria in the overlying waters. Mussels bioaccumulated efficiently, although with different efficiencies, all of the microorganisms studied. Ratios comparing the levels of microorganisms in mussels were determined. These ratios changed in mussels collected at the different sites. They suggest that bacteriophages infecting B. fragilis and somatic coliphages have the lowest decay rates among the microorganisms studied, with the exception of Clostridium perfringens. On the contrary, concentrations of F-specific coliphages showed a greater rate of decay than the other bacteriophages at sites more distant from the focus of contamination. Additionally, levels of enteroviruses were studied in a number of samples, and in these samples, the B. fragilis bacteriophages clearly outnumbered the enteroviruses. The results of this study indicate that, under the environmental conditions studied, the fate of phages infecting B. fragilis released into the marine environment resembles that of human viruses more than any other microorganism examined. Images PMID:8074509

  1. Analysis of the outer membrane proteome and secretome of Bacteroides fragilis reveals a multiplicity of secretion mechanisms.

    PubMed

    Wilson, Marlena M; Anderson, D Eric; Bernstein, Harris D

    2015-01-01

    Bacteroides fragilis is a widely distributed member of the human gut microbiome and an opportunistic pathogen. Cell surface molecules produced by this organism likely play important roles in colonization, communication with other microbes, and pathogenicity, but the protein composition of the outer membrane (OM) and the mechanisms used to transport polypeptides into the extracellular space are poorly characterized. Here we used LC-MS/MS to analyze the OM proteome and secretome of B. fragilis NCTC 9343 grown under laboratory conditions. Of the 229 OM proteins that we identified, 108 are predicted to be lipoproteins, and 61 are predicted to be TonB-dependent transporters. Based on their proximity to genes encoding TonB-dependent transporters, many of the lipoprotein genes likely encode proteins involved in nutrient or small molecule uptake. Interestingly, protease accessibility and biotinylation experiments indicated that an unusually large fraction of the lipoproteins are cell-surface exposed. We also identified three proteins that are members of a novel family of autotransporters, multiple potential type I protein secretion systems, and proteins that appear to be components of a type VI secretion apparatus. The secretome consisted of lipoproteins and other proteins that might be substrates of the putative type I or type VI secretion systems. Our proteomic studies show that B. fragilis differs considerably from well-studied Gram-negative bacteria such as Escherichia coli in both the spectrum of OM proteins that it produces and the range of secretion strategies that it utilizes. PMID:25658944

  2. A scissor blade-like closing mechanism implicated in transmembrane signaling in a Bacteroides hybrid two-component system

    PubMed Central

    Lowe, Elisabeth C.; Baslé, Arnaud; Czjzek, Mirjam; Firbank, Susan J.; Bolam, David N.

    2012-01-01

    Signaling across the membrane in response to extracellular stimuli is essential for survival of all cells. In bacteria, responses to environmental changes are predominantly mediated by two-component systems, which are typically composed of a membrane-spanning sensor histidine kinase and a cytoplasmic response regulator. In the human gut symbiont Bacteroides thetaiotaomicron, hybrid two-component systems are a key part of the bacterium’s ability to sense and degrade complex carbohydrates in the gut. Here, we identify the activating ligand of the hybrid two-component system, BT4663, which controls heparin and heparan sulfate acquisition and degradation in this prominent gut microbe, and report the crystal structure of the extracellular sensor domain in both apo and ligand-bound forms. Current models for signal transduction across the membrane involve either a piston-like or rotational displacement of the transmembrane helices to modulate activity of the linked cytoplasmic kinases. The structures of the BT4663 sensor domain reveal a significant conformational change in the homodimer on ligand binding, which results in a scissor-like closing of the C-termini of each protomer. We propose this movement activates the attached intracellular kinase domains and represents an allosteric mechanism for bacterial transmembrane signaling distinct from previously described models, thus expanding our understanding of signal transduction across the membrane, a fundamental requirement in many important biological processes. PMID:22532667

  3. Use of a unique gene sequence as a probe to enumerate a strain of Bacteroides ruminicola introduced into the rumen.

    PubMed Central

    Attwood, G T; Lockington, R A; Xue, G P; Brooker, J D

    1988-01-01

    Cloned fragments of genomic DNA from the ruminal anaerobe Bacteroides ruminicola subsp. brevis B14 were isolated and used as hybridization probes to identify closely related bacterial species. One DNA fragment unique to strain B14 was tested to determine its sensitivity in detecting homologous sequences among total ruminal microbial DNA. In a DNA titration experiment, the probe was capable of detecting strain B14 sequences in vitro down to 0.1% of the total bacterial DNA present in a hybridization assay. There was no detectable signal for total ruminal bacterial DNA. The specificity of this DNA fragment was exploited to enumerate strain B14 in a fresh mixed suspension of ruminal bacteria in vitro and after inoculation of the strain into the rumen. In vitro strain B14 had a half-life of 9 h. However, following inoculation into the rumen there was a very rapid loss of the strain to below the detectable limit within 3 h. The half-life was less than 30 min. This loss was not due to ruminal dilution or to bacteriophage attack but was possibly the result of a specific bacteriocinlike activity present in the rumen and detectable in fresh ruminal fluid. Images PMID:3355138

  4. Unraveling the substrate recognition mechanism and specificity of the unusual glycosyl hydrolase family 29 BT2192 from Bacteroides thetaiotaomicron.

    PubMed

    Guillotin, Laure; Lafite, Pierre; Daniellou, Richard

    2014-03-11

    Glycosyl hydrolase (GH) family 29 (CAZy database) consists of retaining α-l-fucosidases. We have identified BT2192, a protein from Bacteroides thetaiotaomicron, as the first GH29 representative exhibiting both weak α-l-fucosidase and β-d-galactosidase activities. Determination and analysis of X-ray structures of BT2192 in complex with β-d-galactoside competitive inhibitors showed a new binding mode different from that of known GH29 enzymes. Three point mutations, specific to BT2192, prevent the canonical GH29 substrate α-l-fucose from binding efficiently to the fucosidase-like active site relative to other GH29 enzymes. β-d-Galactoside analogues bind and interact in a second pocket, which is not visible in other reported GH29 structures. Molecular simulations helped in the assessment of the flexibility of both substrates in their respective pocket. Hydrolysis of the fucosyl moiety from the putative natural substrates like 3-fucosyllactose or Lewis(X) antigen would be mainly due to the efficient interactions with the galactosyl moiety, in the second binding site, located more than 6-7 Å apart. PMID:24527659

  5. Expression of arsenic resistance genes in the obligate anaerobe Bacteroides vulgatus ATCC 8482, a gut microbiome bacterium.

    PubMed

    Li, Jiaojiao; Mandal, Goutam; Rosen, Barry P

    2016-06-01

    The response of the obligate anaerobe Bacteroides vulgatus ATCC 8482, a common human gut microbiota, to arsenic was determined. B. vulgatus ATCC 8482 is highly resistant to pentavalent As(V) and methylarsenate (MAs(V)). It is somewhat more sensitive to trivalent inorganic As(III) but 100-fold more sensitive to methylarsenite (MAs(III)) than to As(III). B. vulgatus ATCC 8482 has eight continuous genes in its genome that we demonstrate form an arsenical-inducible transcriptional unit. The first gene of this ars operon, arsR, encodes a putative ArsR As(III)-responsive transcriptional repressor. The next three genes encode proteins of unknown function. The remaining genes, arsDABC, have well-characterized roles in detoxification of inorganic arsenic, but there are no known genes for MAs(III) resistance. Expression of each gene after exposure to trivalent and pentavalent inorganic and methylarsenicals was analyzed. MAs(III) was the most effective inducer. The arsD gene was the most highly expressed of the ars operon genes. These results demonstrate that this anaerobic microbiome bacterium has arsenic-responsive genes that confer resistance to inorganic arsenic and may be responsible for the organism's ability to maintain its prevalence in the gut following dietary exposure to inorganic arsenic. PMID:27040269

  6. Monocolonization of Germ-Free Mice with Bacteroides fragilis Protects against Dextran Sulfate Sodium-Induced Acute Colitis

    PubMed Central

    Liu, Ju-Yun; Li, Yen-Peng; Huang, Yen-Te; Chuang, Hsiao-Li

    2014-01-01

    Ulcerative colitis is inflammatory conditions of the colon caused by interplay of genetic and environmental factors. Previous studies indicated that the gut microflora may be involved in the colonic inflammation. Bacteroides fragilis (BF) is a Gram-negative anaerobe belonging to the colonic symbiotic. We aimed to investigate the protective role of BF in a colitis model induced in germ-free (GF) mice by dextran sulfate sodium (DSS). GF C57BL/6JNarl mice were colonized with BF for 28 days before acute colitis was induced by DSS. BF colonization significantly increased animal survival by 40%, with less reduction in colon length, and decreased infiltration of inflammatory cells (macrophages and neutrophils) in colon mucosa following challenge with DSS. In addition, BF could enhance the mRNA expression of anti-inflammatory-related cytokine such as interleukin 10 (IL-10) with polymorphism cytokine IL-17 and diminish that of proinflammatory-related tumor necrosis factor α with inducible nitric oxide synthase in the ulcerated colon. Myeloperoxidase activity was also decreased in BF-DSS mice. Taking these together, the BF colonization significantly ameliorated DSS-induced colitis by suppressing the activity of inflammatory-related molecules and inducing the production of anti-inflammatory cytokines. BF may play an important role in maintaining intestinal immune system homeostasis and regulate inflammatory responses. PMID:24971344

  7. Toxicity of Methylated Bismuth Compounds Produced by Intestinal Microorganisms to Bacteroides thetaiotaomicron, a Member of the Physiological Intestinal Microbiota

    PubMed Central

    Bialek, Beatrix; Diaz-Bone, Roland A.; Pieper, Dominik; Hollmann, Markus; Hensel, Reinhard

    2011-01-01

    Methanoarchaea have an outstanding capability to methylate numerous metal(loid)s therefore producing toxic and highly mobile derivatives. Here, we report that the production of methylated bismuth species by the methanoarchaeum Methanobrevibacter smithii, a common member of the human intestine, impairs the growth of members of the beneficial intestinal microbiota at low concentrations. The bacterium Bacteroides thetaiotaomicron, which is of great importance for the welfare of the host due to its versatile digestive abilities and its protective function for the intestine, is highly sensitive against methylated, but not against inorganic, bismuth species. The level of methylated bismuth species produced by the methanoarchaeum M. smithii in a coculture experiment causes a reduction of the maximum cell density of B. thetaiotaomicron. This observation suggests that the production of methylated organometal(loid) species in the human intestine, caused by the activity of methanoarchaea, may affect the health of the host. The impact of the species to reduce the number of the physiological intestinal microbiota brings an additional focus on the potentially harmful role of methanoarchaea in the intestine of a higher organism. PMID:21966291

  8. Reactivity of sera from sheep immunised with individual outer membrane proteins of Bacteroides nodosus against heterologous bacterial strains.

    PubMed

    Emery, D L

    1984-09-01

    In order to identify those bacterial antigens which might be involved in immunity against ovine footrot, antisera were raised in sheep to 6 proteins in the outer membrane complex (OMC) of one strain of Bacteroides nodosus. Examination of the specificity of these antisera by Western blotting, crossed immunoelectrophoresis (XIEP) and IEP, revealed that they recognized the homologous OMC protein, but did not precipitate either undenatured pili or OMC, nor could they agglutinate the homologous bacteria. In contrast, anti-OMC and anti-pili sera could precipitate OMC or pili respectively, and agglutinate whole bacteria. Subsequent analysis of these sera against 5 strains of B. nodosus from different serogroups revealed that Proteins 1, 3 and 4 had a similar antigenic structure in all strains examined. The reactivity of anti-pili sera was restricted to homologous bacteria whereas anti-pilin sera (raised against denatured pili) also reacted with pilin from 2 of 3 heterologous strains. However, none of the patterns of staining or absorption of any of these sera matched the spectrum of cross-protection afforded by vaccination of sheep with B. nodosus strain 198 cells. The results question the role of individual OMC proteins in cross-protective immunity and may imply that interactions between several bacterial components are involved in the phenomenon. PMID:6208674

  9. Mutants of Rhizobium tropici strain CIAT899 that do not induce chlorosis in plants.

    PubMed

    O'Connell, K P; Raffel, S J; Saville, B J; Handelsman, J

    1998-09-01

    Type B strains of Rhizobium tropici induce severe foliar chlorosis when applied at planting to seeds of symbiotic host and non-host dicotyledonous plants. A Tn5-induced mutant, designated CT4812, or R. tropici strain CIAT899 that was unable to induce chlorosis was isolated. Cloning and sequencing of the DNA flanking the transposon in CT4812 revealed that the Tn5 insertion is located in a gene similar to glnD, which encodes uridylyltransferase/uridylyl-removing enzyme in enteric bacteria. Two marker-exchange mutants with insertions in glnD also failed to induce chlorosis in bean (Phaseolus vulgaris) plants. The 5'-most insertion in glnD (in mutant strain ME330) abolished the ability of R. tropici to utilize nitrate as a sole carbon source, whereas a mutation in glnD further downstream (in mutant strain ME245) did not have an obvious effect on nitrate utilization. A gene similar to the Salmonella typhimurium virulence gene mviN overlaps the 3' end of the R. tropici glnD homologue. A mutation in mviN had no effect on the ability of CIAT899 to induce chlorosis in bean plants. Therefore the glnD homologue, but not mviN, appears to be required for induction of chlorosis in plants by R. tropici strain CIAT899. A high nitrogen: carbon ratio in the rhizosphere of bean plants also prevented R. tropici from inducing chlorosis in bean plants. Mutations in either the glnD homologue or mviN had no significant effect on root nodule formation or acetylene reduction activity. A mutation in mviN eliminated motility in R. tropici. The sequence data, the inability of the glnD mutant to utilize nitrate, and the role of the R. tropici glnD gene in chlorosis induction in plants, a process that is nitrogen regulated, suggest that glnD plays a role in nitrogen sensing in R. tropici as its homologues do in other organisms. PMID:9782510

  10. The micro-RNA72c-APETALA2-1 node as a key regulator of the common bean-Rhizobium etli nitrogen fixation symbiosis.

    PubMed

    Nova-Franco, Bárbara; Íñiguez, Luis P; Valdés-López, Oswaldo; Alvarado-Affantranger, Xochitl; Leija, Alfonso; Fuentes, Sara I; Ramírez, Mario; Paul, Sujay; Reyes, José L; Girard, Lourdes; Hernández, Georgina

    2015-05-01

    Micro-RNAs are recognized as important posttranscriptional regulators in plants. The relevance of micro-RNAs as regulators of the legume-rhizobia nitrogen-fixing symbiosis is emerging. The objective of this work was to functionally characterize the role of micro-RNA172 (miR172) and its conserved target APETALA2 (AP2) transcription factor in the common bean (Phaseolus vulgaris)-Rhizobium etli symbiosis. Our expression analysis revealed that mature miR172c increased upon rhizobial infection and continued increasing during nodule development, reaching its maximum in mature nodules and decaying in senescent nodules. The expression of AP2-1 target showed a negative correlation with miR172c expression. A drastic decrease in miR172c and high AP2-1 mRNA levels were observed in ineffective nodules. Phenotypic analysis of composite bean plants with transgenic roots overexpressing miR172c or a mutated AP2-1 insensitive to miR172c cleavage demonstrated the pivotal regulatory role of the miR172 node in the common bean-rhizobia symbiosis. Increased miR172 resulted in improved root growth, increased rhizobial infection, increased expression of early nodulation and autoregulation of nodulation genes, and improved nodulation and nitrogen fixation. In addition, these plants showed decreased sensitivity to nitrate inhibition of nodulation. Through transcriptome analysis, we identified 114 common bean genes that coexpressed with AP2-1 and proposed these as being targets for transcriptional activation by AP2-1. Several of these genes are related to nodule senescence, and we propose that they have to be silenced, through miR172c-induced AP2-1 cleavage, in active mature nodules. Our work sets the basis for exploring the miR172-mediated improvement of symbiotic nitrogen fixation in common bean, the most important grain legume for human consumption. PMID:25739700

  11. The Micro-RNA172c-APETALA2-1 Node as a Key Regulator of the Common Bean-Rhizobium etli Nitrogen Fixation Symbiosis1[OPEN

    PubMed Central

    Nova-Franco, Bárbara; Íñiguez, Luis P.; Valdés-López, Oswaldo; Leija, Alfonso; Fuentes, Sara I.; Ramírez, Mario; Paul, Sujay

    2015-01-01

    Micro-RNAs are recognized as important posttranscriptional regulators in plants. The relevance of micro-RNAs as regulators of the legume-rhizobia nitrogen-fixing symbiosis is emerging. The objective of this work was to functionally characterize the role of micro-RNA172 (miR172) and its conserved target APETALA2 (AP2) transcription factor in the common bean (Phaseolus vulgaris)-Rhizobium etli symbiosis. Our expression analysis revealed that mature miR172c increased upon rhizobial infection and continued increasing during nodule development, reaching its maximum in mature nodules and decaying in senescent nodules. The expression of AP2-1 target showed a negative correlation with miR172c expression. A drastic decrease in miR172c and high AP2-1 mRNA levels were observed in ineffective nodules. Phenotypic analysis of composite bean plants with transgenic roots overexpressing miR172c or a mutated AP2-1 insensitive to miR172c cleavage demonstrated the pivotal regulatory role of the miR172 node in the common bean-rhizobia symbiosis. Increased miR172 resulted in improved root growth, increased rhizobial infection, increased expression of early nodulation and autoregulation of nodulation genes, and improved nodulation and nitrogen fixation. In addition, these plants showed decreased sensitivity to nitrate inhibition of nodulation. Through transcriptome analysis, we identified 114 common bean genes that coexpressed with AP2-1 and proposed these as being targets for transcriptional activation by AP2-1. Several of these genes are related to nodule senescence, and we propose that they have to be silenced, through miR172c-induced AP2-1 cleavage, in active mature nodules. Our work sets the basis for exploring the miR172-mediated improvement of symbiotic nitrogen fixation in common bean, the most important grain legume for human consumption. PMID:25739700

  12. Degradation of Fructans and Production of Propionic Acid by Bacteroides thetaiotaomicron are Enhanced by the Shortage of Amino Acids.

    PubMed

    Adamberg, Signe; Tomson, Katrin; Vija, Heiki; Puurand, Marju; Kabanova, Natalja; Visnapuu, Triinu; Jõgi, Eerik; Alamäe, Tiina; Adamberg, Kaarel

    2014-01-01

    Bacteroides thetaiotaomicron is commonly found in the human colon and stabilizes its ecosystem by catabolism of various polysaccharides. A model of cross-talk between the metabolism of amino acids and fructans in B. thetaiotaomicron was proposed. The growth of B. thetaiotaomicron DSM 2079 in two defined media containing mineral salts and vitamins, and supplemented with either 20 or 2 amino acids, was studied in an isothermal microcalorimeter. The polyfructans inulin (from chicory) and levan (synthesized using levansucrase from Pseudomonas syringae), two fructooligosaccharide preparations with different composition, sucrose and fructose were tested as substrates. The calorimetric power-time curves were substrate specific and typically multiauxic. A surplus of amino acids reduced the consumption of longer oligosaccharides (degree of polymerization > 3). Bacterial growth was not detected either in the carbohydrate free medium containing amino acids or in the medium with inulin as a sole carbohydrate. In amino acid-restricted medium, fermentation leading to acetic acid formation was dominant at the beginning of growth (up to 24 h), followed by increased lactic acid production, and mainly propionic and succinic acids were produced at the end of fermentation. In the medium supplemented with 20 amino acids, the highest production of d-lactate (82 ± 33 mmol/gDW) occurred in parallel with extensive consumption (up to 17 mmol/gDW) of amino acids, especially Ser, Thr, and Asp. The production of Ala and Glu was observed at growth on all substrates, and the production was enhanced under amino acid deficiency. The study revealed the influence of amino acids on fructan metabolism in B. thetaiotaomicron and showed that defined growth media are invaluable in elucidating quantitative metabolic profiles of the bacteria. Levan was shown to act as an easily degradable substrate for B. thetaiotaomicron. The effect of levan on balancing or modifying colon microbiota will

  13. Structure of the GH76 α-mannanase homolog, BT2949, from the gut symbiont Bacteroides thetaiotaomicron

    PubMed Central

    Thompson, Andrew J.; Cuskin, Fiona; Spears, Richard J.; Dabin, Jerome; Turkenburg, Johan P.; Gilbert, Harry J.; Davies, Gideon J.

    2015-01-01

    The large bowel microbiota, a complex ecosystem resident within the gastrointestinal tract of all human beings and large mammals, functions as an essential, nonsomatic metabolic organ, hydrolysing complex dietary polysaccharides and modulating the host immune system to adequately tolerate ingested antigens. A significant member of this community, Bacteroides thetaiotaomicron, has evolved a complex system for sensing and processing a wide variety of natural glycoproducts in such a way as to provide maximum benefit to itself, the wider microbial community and the host. The immense ability of B. thetaiotaomicron as a ‘glycan specialist’ resides in its enormous array of carbohydrate-active enzymes, many of which are arranged into polysaccharide-utilization loci (PULs) that are able to degrade sugar polymers that are often inaccessible to other gut residents, notably α-mannan. The B. thetaiotaomicron genome encodes ten putative α-mannanases spread across various PULs; however, little is known about the activity of these enzymes or the wider implications of α-mannan metabolism for the health of both the microbiota and the host. In this study, SAD phasing of a selenomethionine derivative has been used to investigate the structure of one such B. thetaiotaomicron enzyme, BT2949, which belongs to the GH76 family of α-mannanases. BT2949 presents a classical (α/α)6-barrel structure comprising a large extended surface cleft common to other GH76 family members. Analysis of the structure in conjunction with sequence alignments reveals the likely location of the catalytic active site of this noncanonical GH76. PMID:25664752

  14. Structure of the GH76 α-mannanase homolog, BT2949, from the gut symbiont Bacteroides thetaiotaomicron

    SciTech Connect

    Thompson, Andrew J.; Cuskin, Fiona; Spears, Richard J.; Dabin, Jerome; Turkenburg, Johan P.; Gilbert, Harry J.; Davies, Gideon J.

    2015-02-01

    A high-resolution structure of a noncanonical α-mannanase relevant to human health and nutrition has been solved via heavy-atom phasing of a selenomethionine derivative. The large bowel microbiota, a complex ecosystem resident within the gastrointestinal tract of all human beings and large mammals, functions as an essential, nonsomatic metabolic organ, hydrolysing complex dietary polysaccharides and modulating the host immune system to adequately tolerate ingested antigens. A significant member of this community, Bacteroides thetaiotaomicron, has evolved a complex system for sensing and processing a wide variety of natural glycoproducts in such a way as to provide maximum benefit to itself, the wider microbial community and the host. The immense ability of B. thetaiotaomicron as a ‘glycan specialist’ resides in its enormous array of carbohydrate-active enzymes, many of which are arranged into polysaccharide-utilization loci (PULs) that are able to degrade sugar polymers that are often inaccessible to other gut residents, notably α-mannan. The B. thetaiotaomicron genome encodes ten putative α-mannanases spread across various PULs; however, little is known about the activity of these enzymes or the wider implications of α-mannan metabolism for the health of both the microbiota and the host. In this study, SAD phasing of a selenomethionine derivative has been used to investigate the structure of one such B. thetaiotaomicron enzyme, BT2949, which belongs to the GH76 family of α-mannanases. BT2949 presents a classical (α/α){sub 6}-barrel structure comprising a large extended surface cleft common to other GH76 family members. Analysis of the structure in conjunction with sequence alignments reveals the likely location of the catalytic active site of this noncanonical GH76.

  15. Phylogenetic characterization and in situ detection of a Cytophaga-Flexibacter-Bacteroides phylogroup bacterium in Tuber borchii vittad. Ectomycorrhizal mycelium.

    PubMed

    Barbieri, E; Potenza, L; Rossi, I; Sisti, D; Giomaro, G; Rossetti, S; Beimfohr, C; Stocchi, V

    2000-11-01

    Mycorrhizal ascomycetous fungi are obligate ectosymbionts that colonize the roots of gymnosperms and angiosperms. In this paper we describe a straightforward approach in which a combination of morphological and molecular methods was used to survey the presence of potentially endo- and epiphytic bacteria associated with the ascomycetous ectomycorrhizal fungus Tuber borchii Vittad. Universal eubacterial primers specific for the 5' and 3' ends of the 16S rRNA gene (16S rDNA) were used for PCR amplification, direct sequencing, and phylogenetic analyses. The 16S rDNA was amplified directly from four pure cultures of T. borchii Vittad. mycelium. A nearly full-length sequence of the gene coding for the prokaryotic small-subunit rRNA was obtained from each T. borchii mycelium studied. The 16S rDNA sequences were almost identical (98 to 99% similarity), and phylogenetic analysis placed them in a single unique rRNA branch belonging to the Cytophaga-Flexibacter-Bacteroides (CFB) phylogroup which had not been described previously. In situ detection of the CFB bacterium in the hyphal tissue of the fungus T. borchii was carried out by using 16S rRNA-targeted oligonucleotide probes for the eubacterial domain and the Cytophaga-Flexibacter phylum, as well as a probe specifically designed for the detection of this mycelium-associated bacterium. Fluorescent in situ hybridization showed that all three of the probes used bound to the mycelium tissue. This study provides the first direct visual evidence of a not-yet-cultured CFB bacterium associated with a mycorrhizal fungus of the genus Tuber. PMID:11055961

  16. Phylogenetic Characterization and In Situ Detection of a Cytophaga-Flexibacter-Bacteroides Phylogroup Bacterium in Tuber borchii Vittad. Ectomycorrhizal Mycelium

    PubMed Central

    Barbieri, Elena; Potenza, Lucia; Rossi, Ismaela; Sisti, Davide; Giomaro, Giovanna; Rossetti, Simona; Beimfohr, Claudia; Stocchi, Vilberto

    2000-01-01

    Mycorrhizal ascomycetous fungi are obligate ectosymbionts that colonize the roots of gymnosperms and angiosperms. In this paper we describe a straightforward approach in which a combination of morphological and molecular methods was used to survey the presence of potentially endo- and epiphytic bacteria associated with the ascomycetous ectomycorrhizal fungus Tuber borchii Vittad. Universal eubacterial primers specific for the 5′ and 3′ ends of the 16S rRNA gene (16S rDNA) were used for PCR amplification, direct sequencing, and phylogenetic analyses. The 16S rDNA was amplified directly from four pure cultures of T. borchii Vittad. mycelium. A nearly full-length sequence of the gene coding for the prokaryotic small-subunit rRNA was obtained from each T. borchii mycelium studied. The 16S rDNA sequences were almost identical (98 to 99% similarity), and phylogenetic analysis placed them in a single unique rRNA branch belonging to the Cytophaga-Flexibacter-Bacteroides (CFB) phylogroup which had not been described previously. In situ detection of the CFB bacterium in the hyphal tissue of the fungus T. borchii was carried out by using 16S rRNA-targeted oligonucleotide probes for the eubacterial domain and the Cytophaga-Flexibacter phylum, as well as a probe specifically designed for the detection of this mycelium-associated bacterium. Fluorescent in situ hybridization showed that all three of the probes used bound to the mycelium tissue. This study provides the first direct visual evidence of a not-yet-cultured CFB bacterium associated with a mycorrhizal fungus of the genus Tuber. PMID:11055961

  17. Bacteroides fragilis type VI secretion systems use novel effector and immunity proteins to antagonize human gut Bacteroidales species.

    PubMed

    Chatzidaki-Livanis, Maria; Geva-Zatorsky, Naama; Comstock, Laurie E

    2016-03-29

    Type VI secretion systems (T6SSs) are multiprotein complexes best studied in Gram-negative pathogens where they have been shown to inhibit or kill prokaryotic or eukaryotic cells and are often important for virulence. We recently showed that T6SS loci are also widespread in symbiotic human gut bacteria of the order Bacteroidales, and that these T6SS loci segregate into three distinct genetic architectures (GA). GA1 and GA2 loci are present on conserved integrative conjugative elements (ICE) and are transferred and shared among diverse human gut Bacteroidales species. GA3 loci are not contained on conserved ICE and are confined toBacteroides fragilis Unlike GA1 and GA2 T6SS loci, most GA3 loci do not encode identifiable effector and immunity proteins. Here, we studied GA3 T6SSs and show that they antagonize most human gut Bacteroidales strains analyzed, except forB. fragilisstrains with the same T6SS locus. A combination of mutation analyses,trans-protection analyses, and in vitro competition assays, allowed us to identify novel effector and immunity proteins of GA3 loci. These proteins are not orthologous to known proteins, do not contain identified motifs, and most have numerous predicted transmembrane domains. Because the genes encoding effector and immunity proteins are contained in two variable regions of GA3 loci, GA3 T6SSs of the speciesB. fragilisare likely the source of numerous novel effector and immunity proteins. Importantly, we show that the GA3 T6SS of strain 638R is functional in the mammalian gut and provides a competitive advantage to this organism. PMID:26951680

  18. Degradation of Fructans and Production of Propionic Acid by Bacteroides thetaiotaomicron are Enhanced by the Shortage of Amino Acids

    PubMed Central

    Adamberg, Signe; Tomson, Katrin; Vija, Heiki; Puurand, Marju; Kabanova, Natalja; Visnapuu, Triinu; Jõgi, Eerik; Alamäe, Tiina; Adamberg, Kaarel

    2014-01-01

    Bacteroides thetaiotaomicron is commonly found in the human colon and stabilizes its ecosystem by catabolism of various polysaccharides. A model of cross-talk between the metabolism of amino acids and fructans in B. thetaiotaomicron was proposed. The growth of B. thetaiotaomicron DSM 2079 in two defined media containing mineral salts and vitamins, and supplemented with either 20 or 2 amino acids, was studied in an isothermal microcalorimeter. The polyfructans inulin (from chicory) and levan (synthesized using levansucrase from Pseudomonas syringae), two fructooligosaccharide preparations with different composition, sucrose and fructose were tested as substrates. The calorimetric power-time curves were substrate specific and typically multiauxic. A surplus of amino acids reduced the consumption of longer oligosaccharides (degree of polymerization > 3). Bacterial growth was not detected either in the carbohydrate free medium containing amino acids or in the medium with inulin as a sole carbohydrate. In amino acid-restricted medium, fermentation leading to acetic acid formation was dominant at the beginning of growth (up to 24 h), followed by increased lactic acid production, and mainly propionic and succinic acids were produced at the end of fermentation. In the medium supplemented with 20 amino acids, the highest production of d-lactate (82 ± 33 mmol/gDW) occurred in parallel with extensive consumption (up to 17 mmol/gDW) of amino acids, especially Ser, Thr, and Asp. The production of Ala and Glu was observed at growth on all substrates, and the production was enhanced under amino acid deficiency. The study revealed the influence of amino acids on fructan metabolism in B. thetaiotaomicron and showed that defined growth media are invaluable in elucidating quantitative metabolic profiles of the bacteria. Levan was shown to act as an easily degradable substrate for B. thetaiotaomicron. The effect of levan on balancing or modifying colon microbiota will

  19. Peptide Sequence Region That is Essential for the Interactions of the Enterotoxigenic Bacteroides fragilis Metalloproteinase II with E-cadherin

    PubMed Central

    Shiryaev, Sergey A.; Remacle, Albert G.; Cieplak, Piotr; Strongin, Alex Y.

    2015-01-01

    Bacteroides fragilis is a valuable anaerobic commensal and an essential component of the gut microbiome in humans. The presence of a short pathogenicity island in the genome is predominantly associated with the enterotoxigenic strains of B. fragilis. Metallopro-teinase II (MPII) and fragilysin (FRA) are the structurally related enzymes encoded by the pathogenicity island in the enterotoxigenic strains. Accordingly, there is a significant overlap between the cleavage preferences of MPII and FRA. These proteinases, however, are counter-transcribed in the bacterial genome suggesting their distinct and specialized functions in the course of infection. It is well established that FRA directly cleaves E-cadherin, a key protein of the cell-to-cell adhesion junctions in the intestinal epithelium. Counterintuitively, MPII directly binds to, rather than cleaves, E-cadherin. Structural modeling suggested that a potential E-cadherin binding site involves the C-terminal -helical region of the MPII catalytic domain. The sequence of this region is different in MPII and FRA. Here, we employed substitution mutagenesis of this C-terminal -helical region to isolate the MPII mutants with the potentially inactivated E-cadherin binding site. Overall, as a result of our modeling, mutagenesis and binding studies, we determined that the C-terminal ten residue segment is essential for the binding of MPII, but not of FRA3, to E-cadherin, and that the resulting MPII•E-cadherin complex does not impair E-cadherin-dependent cell-to-cell contacts. It is possible to envision that the putative cleavage targets of MPII should be explored not only on the host cell surface but also in B. fragilis. PMID:25964952

  20. Human immunoglobulin G antibody response to iron-repressible and other membrane proteins of Porphyromonas (Bacteroides) gingivalis.

    PubMed Central

    Chen, C K; DeNardin, A; Dyer, D W; Genco, R J; Neiders, M E

    1991-01-01

    The human immunoglobulin G (IgG) immune response against Porphyromonas (Bacteroides) gingivalis A7A1-28 iron-repressible membrane proteins (IRMPs) and other membrane proteins was examined by immunoblot analysis. Thirty sera from patients with adult periodontitis and 30 sera from periodontally healthy subjects were included. Iron limitation of P. gingivalis was achieved by growing bacteria in brain heart infusion broth supplemented with protoporphyrin IX and 250 microM alpha, alpha'-dypyridyl, a ferrous iron chelator. Iron-sufficient growth was achieved by growing bacteria in the same medium without alpha, alpha'-dypyridyl. Human sera, in particular those from patients with periodontitis who exhibited high levels of IgG against whole cells of P. gingivalis A7A1-28 in serum in an enzyme-linked immunosorbent assay (ELISA), commonly reacted with five membrane proteins with apparent molecular masses of 80, 67.5, 51, 40.5, and 28 kDa and four IRMPs of 46, 43, 37.5, and 22 kDa. More than 80% of the sera from patients with periodontitis and high levels of IgG against strain A7A1-28 in serum by ELISA reacted with the 46-, 43-, and 37.5-kDa IRMPs, and 40% of these subjects expressed immunoreactivity against the 22-kDa IRMP. Sera from patients with periodontitis and low levels of IgG against strain A7A1-28 in serum by ELISA and sera from periodontally healthy subjects exhibited less immunoreactivity against IRMPs and the five membrane proteins of P. gingivalis. The present study indicates that P. gingivalis IRMPs are immunogenic and that these proteins are expressed in vivo. Images PMID:2050407