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Sample records for rhizobium bacteroid development

  1. [Utilization of nitrate by bacteroids and cytosol of nodules formed by Rhizobium leguminosarum].

    PubMed

    Fernández-López, M; Delgado, M J; Olivares, J; Bedmar, E J

    1989-06-01

    Nitrite production by nodules and roots of pea plants (Pisum sativum L., cultivar Alaska) inoculated with Rhizobium leguminosarum strain 3855 has been studied. Nitrate reductase (NR) activity and nitrite reductase (NiR) activity of the bacteroidal and cytosolic fractions of the nodules were also determined, as well as the nitrite content of the nodules cytosol. Nitrite production by nodules and roots from plants treated with 5 mM KNO3 was higher than that of nodules and roots from plants not treated with nitrate, and regardless of the nitrate treatment, nitrite production increased with the incubation period. The presence of nitrate, propanol or both compounds in the incubation mixtures significantly increased the nitrite production by nodules and roots. Nitrite reductase activity was detected in fresh by isolated bacteroids of R. leguminosarum strain 3855, although the presence of nitrate reductase activity could not be detected both in bacteroids of nodules isolated from plants treated or not with 5 mM KNO3. After isolation, when bacteroids were incubated in a mixture with nitrate, nitrate reductase activity developed after incubation for 12 h. Consequently, there was an increase in nitrite reductase activity, which resulted in the disappearance of the nitrite previously accumulated in the incubation medium. Nitrate utilization by bacteroids was not detected until 5 h from the beginning of the incubation period. Since the presence of chloramphenicol or rifampicin in the incubation medium prevented the development of the nitrate reductase activity, such activity was induced in bacteroids. Nitrite content and nitrate reductase and nitrite reductase activities of the cytosol from nodules of pea plants treated or not with 5 mM KNO3 varied with the buffer used for nodules homogenization. However, no nitrite was found when nodules were homogenized with ethanol, what indicates that nitrite accumulation in the cytosol occurs during the homogenization process of the

  2. Respiratory control determines respiration and nitrogenase activity of Rhizobium leguminosarum bacteroids.

    PubMed

    Haaker, H; Szafran, M; Wassink, H; Klerk, H; Appels, M

    1996-08-01

    The relationship between the O2 input rate into a suspension of Rhizobium leguminosarum bacteroids, the cellular ATP and ADP pools, and the whole-cell nitrogenase activity during L-malate oxidation has been studied. It was observed that inhibition of nitrogenase by excess O2 coincided with an increase of the cellular ATP/ADP ratio. When under this condition the protonophore carbonyl cyanide m-chlorophenylhydrazone (CCCP) was added, the cellular ATP/ADP ratio was lowered while nitrogenase regained activity. To explain these observations, the effects of nitrogenase activity and CCCP on the O2 consumption rate of R. leguminosarum bacteroids were determined. From 100 to 5 microM O2, a decline in the O2 consumption rate was observed to 50 to 70% of the maximal O2 consumption rate. A determination of the redox state of the cytochromes during an O2 consumption experiment indicated that at O2 concentrations above 5 microM, electron transport to the cytochromes was rate-limiting oxidation and not the reaction of reduced cytochromes with oxygen. The kinetic properties of the respiratory chain were determined from the deoxygenation of oxyglobins. In intact cells the maximal deoxygenation activity was stimulated by nitrogenase activity or CCCP. In isolated cytoplasmic membranes NADH oxidation was inhibited by respiratory control. The dehydrogenase activities of the respiratory chain were rate-limiting oxidation at O2 concentrations (if >300 nM. Below 300 nM the terminal oxidase system followed Michaelis-Menten kinetics (Km of 45 +/- 8 nM). We conclude that (i) respiration in R. leguminosarum bacteroids takes place via a respiratory chain terminating at a high-affinity oxidase system, (ii) the activity of the respiratory chain is inhibited by the proton motive force, and (iii) ATP hydrolysis by nitrogenase can partly relieve the inhibition of respiration by the proton motive force and thus stimulate respiration at nanomolar concentrations of O2.

  3. Rhizobium nodM and nodN genes are common nod genes: nodM encodes functions for efficiency of nod signal production and bacteroid maturation.

    PubMed Central

    Baev, N; Schultze, M; Barlier, I; Ha, D C; Virelizier, H; Kondorosi, E; Kondorosi, A

    1992-01-01

    Earlier, we showed that Rhizobium meliloti nodM codes for glucosamine synthase and that nodM and nodN mutants produce strongly reduced root hair deformation activity and display delayed nodulation of Medicago sativa (Baev et al., Mol. Gen. Genet. 228:113-124, 1991). Here, we demonstrate that nodM and nodN genes from Rhizobium leguminosarum biovar viciae restore the root hair deformation activity of exudates of the corresponding R. meliloti mutant strains. Partial restoration of the nodulation phenotypes of these two strains was also observed. In nodulation assays, galactosamine and N-acetylglucosamine could substitute for glucosamine in the suppression of the R. meliloti nodM mutation, although N-acetylglucosamine was less efficient. We observed that in nodules induced by nodM mutants, the bacteroids did not show complete development or were deteriorated, resulting in decreased nitrogen fixation and, consequently, lower dry weights of the plants. This mutant phenotype could also be suppressed by exogenously supplied glucosamine, N-acetylglucosamine, and galactosamine and to a lesser extent by glucosamine-6-phosphate, indicating that the nodM mutant bacteroids are limited for glucosamine. In addition, by using derivatives of the wild type and a nodM mutant in which the nod genes are expressed at a high constitutive level, it was shown that the nodM mutant produces significantly fewer Nod factors than the wild-type strain but that their chemical structures are unchanged. However, the relative amounts of analogs of the cognate Nod signals were elevated, and this may explain the observed host range effects of the nodM mutation. Our data indicate that both the nodM and nodN genes of the two species have common functions and confirm that NodM is a glucosamine synthase with the biochemical role of providing sufficient amounts of the sugar moiety for the synthesis of the glucosamine oligosaccharide signal molecules. Images PMID:1447128

  4. 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.

  5. BacS: an abundant bacteroid protein in Rhizobium etli whose expression ex planta requires nifA.

    PubMed

    Jahn, Olivia J; Davila, Guillermo; Romero, David; Noel, K Dale

    2003-01-01

    Rhizobium etli CFN42 bacteroids from bean nodules possessed an abundant 16-kDa protein (BacS) that was found in the membrane pellet after cell disruption. This protein was not detected in bacteria cultured in tryptone-yeast extract. In minimal media, it was produced at low oxygen concentration but not in a mutant whose nifA was disrupted. N-terminal sequencing of the protein led to isolation of a bacS DNA fragment. DNA hybridization and nucleotide sequencing revealed three copies of the bacS gene, all residing on the main symbiotic plasmid of strain CFN42. A stretch of 304 nucleotides, exactly conserved upstream of all three bacS open reading frames, had very close matches with the NifA and sigma 54 consensus binding sequences. The only bacS homology in the genetic sequence databases was to three hypothetical proteins of unknown function, all from rhizobial species. Mutation and genetic complementation indicated that each of the bacS genes gives rise to a BacS polypeptide. Mutants disrupted or deleted in all three genes did not produce the BacS polypeptide but were Nod+ and Fix+ on Phaseolus vulgaris.

  6. Nickel availability to pea (Pisum sativum L.) plants limits hydrogenase activity of Rhizobium leguminosarum bv. viciae bacteroids by affecting the processing of the hydrogenase structural subunits.

    PubMed Central

    Brito, B; Palacios, J M; Hidalgo, E; Imperial, J; Ruiz-Argüeso, T

    1994-01-01

    Rhizobium leguminosarum bv. viciae UPM791 induces the synthesis of an [NiFe] hydrogenase in pea (Pisum sativum L.) bacteroids which oxidizes the H2 generated by the nitrogenase complex inside the root nodules. The synthesis of this hydrogenase requires the genes for the small and large hydrogenase subunits (hupS and hupL, respectively) and 15 accessory genes clustered in a complex locus in the symbiotic plasmid. We show here that the bacteroid hydrogenase activity is limited by the availability of nickel to pea plants. Addition of Ni2+ to plant nutrient solutions (up to 10 mg/liter) resulted in sharp increases (up to 15-fold) in hydrogenase activity. This effect was not detected when other divalent cations (Zn2+, Co2+, Fe2+, and Mn2+) were added at the same concentrations. Determinations of the steady-state levels of hupSL-specific mRNA indicated that this increase in hydrogenase activity was not due to stimulation of transcription of structural genes. Immunoblot analysis with antibodies raised against the large and small subunits of the hydrogenase enzyme demonstrated that in the low-nickel situation, both subunits are mainly present in slow-migrating, unprocessed forms. Supplementation of the plant nutrient solution with increasing nickel concentrations caused the conversion of the slow-migrating forms of both subunits into fast-moving, mature forms. This nickel-dependent maturation process of the hydrogenase subunits is mediated by accessory gene products, since bacteroids from H2 uptake-deficient mutants carrying Tn5 insertions in hupG and hupK and in hypB and hypE accumulated the immature forms of both hydrogenase subunits even in the presence of high nickel levels. Images PMID:8071205

  7. Early intestinal Bacteroides fragilis colonisation and development of asthma

    PubMed Central

    Vael, Carl; Nelen, Vera; Verhulst, Stijn L; Goossens, Herman; Desager, Kristine N

    2008-01-01

    Background The 'hygiene hypothesis' suggests that early exposure to microbes can be protective against atopic disease. The intestinal microbial flora could operate as an important postnatal regulator of the Th1/Th2 balance. The aim of the study was to investigate the association between early intestinal colonisation and the development of asthma in the first 3 years of life. Methods In a prospective birth cohort, 117 children were classified according to the Asthma Predictive Index. A positive index included wheezing during the first three years of life combined with eczema in the child in the first years of life or with a parental history of asthma. A faecal sample was taken at the age of 3 weeks and cultured on selective media. Results Asthma Predictive Index was positive in 26/117 (22%) of the children. The prevalence of colonisation with Bacteroides fragilis was higher at 3 weeks in index+ compared to index- children (64% vs. 34% p < 0,05). Bacteroides fragilis and Total Anaerobes counts at 3 weeks were significantly higher in children with a positive index as compared with those without. After adjusting for confounders a positive association was found between Bacteroides fragilis colonisation and Asthma Predictive Index (odds ratio: 4,4; confidence interval: 1,7 – 11,8). Conclusion Bacteroides fragilis colonisation at age 3 weeks is an early indicator of possible asthma later in life. This study could provide the means for more accurate targeting of treatment and prevention and thus more effective and better controlled modulation of the microbial milieu. PMID:18822123

  8. The lipopolysaccharide lipid-a long chain fatty acid is important for rhizobium leguminosarum growth and stress adaptation in free-living and nodule environments

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rhizobium bacteria live in soil and plant environments, are capable of inducing symbiotic nodules on legumes, invade these nodules, and develop into bacteroids that fix atmospheric nitrogen into ammonium. Lipopolysaccharide (LPS) is anchored in the bacterial outer membrane through a specialized lipi...

  9. Transcriptomic analysis of Rhizobium leguminosarum biovar viciae in symbiosis with host plants Pisum sativum and Vicia cracca.

    PubMed

    Karunakaran, R; Ramachandran, V K; Seaman, J C; East, A K; Mouhsine, B; Mauchline, T H; Prell, J; Skeffington, A; Poole, P S

    2009-06-01

    Rhizobium leguminosarum bv. viciae forms nitrogen-fixing nodules on several legumes, including pea (Pisum sativum) and vetch (Vicia cracca), and has been widely used as a model to study nodule biochemistry. To understand the complex biochemical and developmental changes undergone by R. leguminosarum bv. viciae during bacteroid development, microarray experiments were first performed with cultured bacteria grown on a variety of carbon substrates (glucose, pyruvate, succinate, inositol, acetate, and acetoacetate) and then compared to bacteroids. Bacteroid metabolism is essentially that of dicarboxylate-grown cells (i.e., induction of dicarboxylate transport, gluconeogenesis and alanine synthesis, and repression of sugar utilization). The decarboxylating arm of the tricarboxylic acid cycle is highly induced, as is gamma-aminobutyrate metabolism, particularly in bacteroids from early (7-day) nodules. To investigate bacteroid development, gene expression in bacteroids was analyzed at 7, 15, and 21 days postinoculation of peas. This revealed that bacterial rRNA isolated from pea, but not vetch, is extensively processed in mature bacteroids. In early development (7 days), there were large changes in the expression of regulators, exported and cell surface molecules, multidrug exporters, and heat and cold shock proteins. fix genes were induced early but continued to increase in mature bacteroids, while nif genes were induced strongly in older bacteroids. Mutation of 37 genes that were strongly upregulated in mature bacteroids revealed that none were essential for nitrogen fixation. However, screening of 3,072 mini-Tn5 mutants on peas revealed previously uncharacterized genes essential for nitrogen fixation. These encoded a potential magnesium transporter, an AAA domain protein, and proteins involved in cytochrome synthesis.

  10. 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.

  11. 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

  12. Development of EUCAST disk diffusion method for susceptibility testing of the Bacteroides fragilis group isolates.

    PubMed

    Nagy, Elisabeth; Justesen, Ulrik Stenz; Eitel, Zsuzsa; Urbán, Edit

    2015-02-01

    With the emergence of antibiotic resistance among Bacteroides fragilis group isolates the need of susceptibility testing in routine laboratories is increasing. The aims of the present study were to evaluate the disk diffusion method for susceptibility testing in case of different clinical isolates of Bacteroides spp by comparing zone diameter results with MICs obtained earlier during an Europe-wide antibiotic susceptibility surveillance, and to propose zone diameter breakpoints, which correlate for the EUCAST MIC breakpoints. We tested 381 clinical isolates of the B. fragilis group to amoxicillin/clavulanic acid, cefoxitin, clindamycin, imipenem, metronidazole, moxifloxacin, piperacillin/tazobactam, tigecycline by agar dilution method previously. The inhibition zones of the same antibiotics including meropenem disc were determined by the disc diffusion on Brucella blood agar supplemented with haemin and vitamin K1. Plates were incubated at 37 °C in an anaerobic atmosphere for 24 h. The zone diameters were read at 100% inhibition. In case of discrepant results MICs were determined by gradient test and compared with the inhibition zones on the same plate. We found a good agreement between the inhibition zone diameters and the MICs for imipenem, metronidazole, moxifloxacin and tigecyclin. The inhibition zone diameters of meropenem also separated clearly the isolates, which can be considered wild-type isolates. In case of amoxicillin/clavulanic acid and piperacillin/tazobactam intermediate and susceptible isolates according to the MIC determination, overlap during the zone diameter determination. Isolates with an inhibition zone <23 mm for amoxicillin/clavulanic acid and <25 mm for piperacillin/tazobactam should be retested by a MIC determination method. The 10 μg clindamycin disc clearly separated the resistant and the susceptible population of B. fragilis group strains. In the case of cefoxitin only resistant population could be separated with an inhibition

  13. Identification of a Novel Gene for Biosynthesis of a Bacteroid-Specific Electron Carrier Menaquinone

    PubMed Central

    Xie, Fuli; Cheng, Guojun; Xu, Hui; Wang, Zhi; Lei, Lei; Li, Youguo

    2011-01-01

    Ubiquinone (UQ) has been considered as an electron mediator in electron transfer that generates ATP in Rhizobium under both free-living and symbiosis conditions. When mutated, the dmtH gene has a symbiotic phenotype of forming ineffective nodules on Astragalus sinicus. The gene was isolated from a Mesorhizobium huakuii 7653R transposon-inserted mutant library. The DNA sequence and conserved protein domain analyses revealed that dmtH encodes demethylmenaquinone (DMK) methyltransferase, which catalyzes the terminal step of menaquinone (MK) biosynthesis. Comparative analysis indicated that dmtH homologs were present in only a few Rhizobia. Real-time quantitative PCR showed dmtH is a bacteroid-specific gene. The highest expression was seen at 25 days after inoculation of strain 7653R. Gene disruption and complementation tests demonstrated that the dmtH gene was essential for bacteroid development and symbiotic nitrogen fixation ability. MK and UQ were extracted from the wild type strain 7653R and mutant strain HK116. MK-7 was accumulated under microaerobic condition and UQ-10 was accumulated under aerobic condition in M. huakuii 7653R. The predicted function of DmtH protein was confirmed by the measurement of methyltransferase activity in vitro. These results revealed that MK-7 was used as an electron carrier instead of UQ in M. huakuii 7653R bacteroids. PMID:22194970

  14. Identification of a novel gene for biosynthesis of a bacteroid-specific electron carrier menaquinone.

    PubMed

    Xie, Fuli; Cheng, Guojun; Xu, Hui; Wang, Zhi; Lei, Lei; Li, Youguo

    2011-01-01

    Ubiquinone (UQ) has been considered as an electron mediator in electron transfer that generates ATP in Rhizobium under both free-living and symbiosis conditions. When mutated, the dmtH gene has a symbiotic phenotype of forming ineffective nodules on Astragalus sinicus. The gene was isolated from a Mesorhizobium huakuii 7653R transposon-inserted mutant library. The DNA sequence and conserved protein domain analyses revealed that dmtH encodes demethylmenaquinone (DMK) methyltransferase, which catalyzes the terminal step of menaquinone (MK) biosynthesis. Comparative analysis indicated that dmtH homologs were present in only a few Rhizobia. Real-time quantitative PCR showed dmtH is a bacteroid-specific gene. The highest expression was seen at 25 days after inoculation of strain 7653R. Gene disruption and complementation tests demonstrated that the dmtH gene was essential for bacteroid development and symbiotic nitrogen fixation ability. MK and UQ were extracted from the wild type strain 7653R and mutant strain HK116. MK-7 was accumulated under microaerobic condition and UQ-10 was accumulated under aerobic condition in M. huakuii 7653R. The predicted function of DmtH protein was confirmed by the measurement of methyltransferase activity in vitro. These results revealed that MK-7 was used as an electron carrier instead of UQ in M. huakuii 7653R bacteroids.

  15. Involvement of the Azorhizobial Chromosome Partition Gene (parA) in the Onset of Bacteroid Differentiation during Sesbania rostrata Stem Nodule Development ▿ †

    PubMed Central

    Liu, Chi-Te; Lee, Kyung-Bum; Wang, Yu-Sheng; Peng, Min-Hua; Lee, Kung-Ta; Suzuki, Shino; Suzuki, Tadahiro; Oyaizu, Hiroshi

    2011-01-01

    A parA gene in-frame deletion mutant of Azorhizobium caulinodans ORS571 (ORS571-ΔparA) was constructed to evaluate the roles of the chromosome-partitioning gene on various bacterial traits and on the development of stem-positioned nodules. The ΔparA mutant showed a pleiomorphic cell shape phenotype and was polyploid, with differences in nucleoid sizes due to dramatic defects in chromosome partitioning. Upon inoculation of the ΔparA mutant onto the stem of Sesbania rostrata, three types of immature nodule-like structures with impaired nitrogen-fixing activity were generated. Most showed signs of bacteroid early senescence. Moreover, the ΔparA cells within the nodule-like structures exhibited multiple developmental-stage phenotypes. Since the bacA gene has been considered an indicator for bacteroid formation, we applied the expression pattern of bacA as a nodule maturity index in this study. Our data indicate that the bacA gene expression is parA dependent in symbiosis. The presence of the parA gene transcript was inversely correlated with the maturity of nodule; the transcript was switched off in fully mature bacteroids. In summary, our experimental evidence demonstrates that the parA gene not only plays crucial roles in cellular development when the microbe is free-living but also negatively regulates bacteroid formation in S. rostrata stem nodules. PMID:21571889

  16. [The Effect of Cadmium on the Efficiency of Development of Legume-Rhizobium Symbiosis].

    PubMed

    Chuhukova, O V; Postrigan, B N; Baimiev, A Kh; Chemeris, A V

    2015-01-01

    Screening of nodule bacteria (rhizobia) forming symbiotic relationships with legumes has been performed in order to isolate strains resistant to cadmium ions in a wide range of concentrations (6-132 mg/kg). The effect ofcadmium salts (6, 12, 24 mg/kg) on the legume-rhizobium symbiosis ofthe pea Pisum sativum L. with Rhizobium leguminosarum and of the fodder galega Galega orientalis Lam. with Rhizobium galegae has been studied under experimental laboratory conditions. No statistically significant differences have been revealed in the growth and biomass of plants with regard to the control in the range of concentrations given above. However, it was found that cadmium inhibited nodulation in P. sativum and stimulated it in G. orientalis.

  17. 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

  18. Morphology of root nodules and nodule-like structures formed by Rhizobium and Agrobacterium strains containing a Rhizobium meliloti megaplasmid

    PubMed Central

    1983-01-01

    We examined expression of the megaplasmid pRme41b of Rhizobium meliloti in two different Rhizobium sp. Strains and in Agrobacterium tumefaciens. Transfer of pRme41b into these bacteria was facilitated by insertion of a recombinant plasmid coding for mobilization functions of RP4 into the nif region (Kondorosi, A., E. Kondorosi, C.E. Pankhurst, W. J. Broughton, and Z. Banfalvi, 1982, Mol. Gen. Genet., 188:433-439). In all cases, transconjugants formed nodule-like structures on the roots of Medicago sativa. These structures were largely composed of meristematic cells but they were not invaded by bacteria. Bacteria were found only within infection threads in root hairs, and within intercellular spaces of the outermost cells of the structures. The donor strain of R. meliloti containing pAK11 or pAK12 in pRme41b initially produced nodules on M. sativa that did not fix nitrogen (Fix- ). In these nodules, bacteria were released from infection threads into the host cells but they did not multiply appreciably. Any bacteroids formed degenerated prematurely. In some cases, however, reversion to a Fix+ phenotype occurred after 4 to 6 wk. Bacteria released into newly infected cells in these nodules showed normal development into bacteriods. PMID:6885919

  19. A Legume TOR Protein Kinase Regulates Rhizobium Symbiosis and Is Essential for Infection and Nodule Development.

    PubMed

    Nanjareddy, Kalpana; Blanco, Lourdes; Arthikala, Manoj-Kumar; Alvarado-Affantranger, Xóchitl; Quinto, Carmen; Sánchez, Federico; Lara, Miguel

    2016-11-01

    The target of rapamycin (TOR) protein kinase regulates metabolism, growth, and life span in yeast, animals, and plants in coordination with nutrient status and environmental conditions. The nutrient-dependent nature of TOR functionality makes this kinase a putative regulator of symbiotic associations involving nutrient acquisition. However, TOR's role in these processes remains to be understood. Here, we uncovered the role of TOR during the bean (Phaseolus vulgaris)-Rhizobium tropici (Rhizobium) symbiotic interaction. TOR was expressed in all tested bean tissues, with higher transcript levels in the root meristems and senesced nodules. We showed TOR promoter expression along the progressing infection thread and in the infected cells of mature nodules. Posttranscriptional gene silencing of TOR using RNA interference (RNAi) showed that this gene is involved in lateral root elongation and root cell organization and also alters the density, size, and number of root hairs. The suppression of TOR transcripts also affected infection thread progression and associated cortical cell divisions, resulting in a drastic reduction of nodule numbers. TOR-RNAi resulted in reduced reactive oxygen species accumulation and altered CyclinD1 and CyclinD3 expression, which are crucial factors for infection thread progression and nodule organogenesis. Enhanced expression of TOR-regulated ATG genes in TOR-RNAi roots suggested that TOR plays a role in the recognition of Rhizobium as a symbiont. Together, these data suggest that TOR plays a vital role in the establishment of root nodule symbiosis in the common bean.

  20. Development of an acute and chronic ecotoxicity assay using lux-marked Rhizobium leguminosarum biovar trifolii.

    PubMed

    Paton, G I; Palmer, G; Burton, M; Rattray, E A; McGrath, S P; Glover, L A; Killham, K

    1997-04-01

    A soil isolate of Rhizobium leguminosarum bv. trifolii was marked with a lux CDABE gene cassette to enable the expression of bioluminescence. The suitability of the bacterium as a soil pollution biosensor was assessed using acute and chronic assays. Bacterial bioluminescence responded sensitively to the metals studied. The order of sensitivity was found to be Cd > Ni = Zn > Cu for the acute test and Cd > Ni = Zn = Cu for the chronic test. The sensitive response of the biosensor highlighted its potential for use as an indicator of soil pollution.

  1. 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

  2. Coordinate expression of hydrogenase and ribulose bisphosphate carboxylase in Rhizobium japonicum Hupc mutants.

    PubMed Central

    Merberg, D; Maier, R J

    1984-01-01

    In contrast to the wild type, H2 uptake-constitutive mutants of Rhizobium japonicum expressed both hydrogenase and ribulose bisphosphate carboxylase activities when grown heterotrophically. However, as bacteroids from soybean root nodules, the H2 uptake-constitutive mutants, like the wild type, did not express ribulose bisphosphate carboxylase activity. PMID:6384199

  3. Exogenous suppression of the symbiotic deficiencies of Rhizobium meliloti exo mutants.

    PubMed Central

    Urzainqui, A; Walker, G C

    1992-01-01

    The acidic exopolysaccharide (EPS I) produced by Rhizobium meliloti during symbiosis with Medicago sativa has been shown to be required for the proper development of nitrogen-fixing nodules. Cloned DNA from the exo region of R. meliloti is shown to stimulate production of the low-molecular-weight form of this exopolysaccharide, and in this report we show that the symbiotic deficiencies of two exo mutants of R. meliloti, the exoA and exoH mutants, can be rescued by the addition of this low-molecular-weight material at the time of inoculation. For exoA and exoH mutants, rescue with a preparation containing low-molecular-weight exopolysaccharide induces the formation of nitrogen-fixing nodules which appear somewhat later and at a reduced efficiency compared with wild-type-induced nodules; however, microscopic analysis of these nodules reveals similar nodule morphology and the presence of large numbers of bacteroids in each. Images PMID:1577707

  4. NUTRITION OF FIVE BACTEROIDES STRAINS

    PubMed Central

    Quinto, Grace

    1962-01-01

    Quinto, Grace (University of Kentucky College of Medicine, Lexington). Nutrition of five Bacteroides strains. J. Bacteriol. 84:559–562. 1962.—Some of the nutritional requirements of five gram-negative anaerobic bacilli, including Ristella perfoetens, Zuberella clostridiformis, and three Bacteroides strains freshly isolated from clinical exudates, were investigated. A fluid maintenance medium was developed in which the three freshly isolated strains, C-4, C-7, and C-2795, grew maximally in 12 to 24 hr. The maintenance medium contained 2.0% Trypticase and Proteose Peptone, 0.5% glucose, and 0.1% sodium thioglycolate; it was adjusted to pH 7.2 and supplemented with 0.1 μg of hemin/ml. Strains C-4, C-7, and C-2795 were cultivated through 14 serial cultures in fluid maintenance medium containing 0.1 μg of hemin/ml. The most satisfactory inoculum was a 1:100 or 1:1,000 dilution of a 24-hr seed culture. All the strains except Z. clostridiformis grew serially in a defined medium. R. perfoetens required pantothenic acid, nicotinic acid, and the following amino acids: histidine, tryptophan, tyrosine, valine, phenylalanine, cystine, and probably arginine, glutamic acid, methionine, glycine, isoleucine, leucine, and lysine. The C-4, C-7, and C-2795 strains required the hemin supplement in defined medium, but not vitamins, purines, or pyrimidines. PMID:13972793

  5. Comparing Symbiotic Efficiency between Swollen versus Nonswollen Rhizobial Bacteroids1[C][W][OA

    PubMed Central

    Oono, Ryoko; Denison, R. Ford

    2010-01-01

    Symbiotic rhizobia differentiate physiologically and morphologically into nitrogen-fixing bacteroids inside legume host nodules. The differentiation is apparently terminal in some legume species, such as peas (Pisum sativum) and peanuts (Arachis hypogaea), likely due to extreme cell swelling induced by the host. In other legume species, such as beans (Phaseolus vulgaris) and cowpeas (Vigna unguiculata), differentiation into bacteroids, which are similar in size and shape to free-living rhizobia, is reversible. Bacteroid modification by plants may affect the effectiveness of the symbiosis. Here, we compare symbiotic efficiency of rhizobia in two different hosts where the rhizobia differentiate into swollen nonreproductive bacteroids in one host and remain nonswollen and reproductive in the other. Two such dual-host strains were tested: Rhizobium leguminosarum A34 in peas and beans and Bradyrhizobium sp. 32H1 in peanuts and cowpeas. In both comparisons, swollen bacteroids conferred more net host benefit by two measures: return on nodule construction cost (plant growth per gram nodule growth) and nitrogen fixation efficiency (H2 production by nitrogenase per CO2 respired). Terminal bacteroid differentiation among legume species has evolved independently multiple times, perhaps due to the increased host fitness benefits observed in this study. PMID:20837702

  6. 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

  7. The Lipopolysaccharide Lipid A Long-Chain Fatty Acid Is Important for Rhizobium leguminosarum Growth and Stress Adaptation in Free-Living and Nodule Environments.

    PubMed

    Bourassa, Dianna V; Kannenberg, Elmar L; Sherrier, D Janine; Buhr, R Jeffrey; Carlson, Russell W

    2017-02-01

    Rhizobium bacteria live in soil and plant environments, are capable of inducing symbiotic nodules on legumes, invade these nodules, and develop into bacteroids that fix atmospheric nitrogen into ammonia. Rhizobial lipopolysaccharide (LPS) is anchored in the bacterial outer membrane through a specialized lipid A containing a very long-chain fatty acid (VLCFA). VLCFA function for rhizobial growth in soil and plant environments is not well understood. Two genes, acpXL and lpxXL, encoding acyl carrier protein and acyltransferase, are among the six genes required for biosynthesis and transfer of VLCFA to lipid A. Rhizobium leguminosarum mutant strains acpXL, acpXL(-)/lpxXL(-), and lpxXL(-) were examined for LPS structure, viability, and symbiosis. Mutations in acpXL and lpxXL abolished VLCFA attachment to lipid A. The acpXL mutant transferred a shorter acyl chain instead of VLCFA. Strains without lpxXL neither added VLCFA nor a shorter acyl chain. In all strains isolated from nodule bacteria, lipid A had longer acyl chains compared with laboratory-cultured bacteria, whereas mutant strains displayed altered membrane properties, modified cationic peptide sensitivity, and diminished levels of cyclic β-glucans. In pea nodules, mutant bacteroids were atypically formed and nitrogen fixation and senescence were affected. The role of VLCFA for rhizobial environmental fitness is discussed.

  8. Development and Partial Characterization of Nearly Isogenic Pea Lines (Pisum sativum L.) that Alter Uptake Hydrogenase Activity in Symbiotic Rhizobium.

    PubMed

    Phillips, D A; Kapulnik, Y; Bedmar, E J; Joseph, C M

    1990-04-01

    Some Rhizobium bacteria have H(2)-uptake (Hup) systems that oxidize H(2) evolved from nitrogenase in leguminous root nodules. Pea (Pisum sativum L.) cultivars ;JI1205' and ;Alaska' produce high Hup (Hup(++)) and moderate Hup (Hup(+)) phenotypes, respectively, in Rhizobium leguminosarum 128C53. The physiological significance and biochemical basis of this host plant genetic effect are unknown. The purpose of this investigation was to advance basic Hup studies by developing nearly isogenic lines of peas that alter Hup phenotypes in R. leguminosarum strains containing hup genes. Eight pairs of nearly isogenic pea lines that produce Hup(++) and Hup(+) phenotypes in R. leguminosarum 128C53 were identified in 173 F(2)-derived F(6) families produced from crosses between JI1205 and Alaska. Tests with the pea isolines and three strains of hup-containing R. leguminosarum showed that the isolines altered Hup activity significantly (P

  9. Bacteroides buccae and related taxa in necrotic root canal infections.

    PubMed Central

    Haapasalo, M

    1986-01-01

    Fifty-seven adults with apical periodontitis were examined for the presence of nonpigmented Bacteroides species in 62 infected root canals. Nonpigmented Bacteroides species were found in 35 canals. In four cases two nonpigmented Bacteroides species and in one case three nonpigmented Bacteroides species were found. Species belonging to the B. fragilis group were not isolated. The most frequently isolated species were B. buccae (15 strains), B. oris (12 strains), and B. oralis (7 strains). alpha-Fucosidase, beta-N-acetylglucosaminidase, and beta-xylosidase appeared to be useful in the identification of B. buccae and B. oris. Corroding Bacteroides species were not found; all corroding strains were identified as Wolinella recta. The occurrence of nonpigmented Bacteroides species was compared with the severity of the periapical infection. A total of 13 B. buccae strains were found in acute infections and only 2 strains were found in asymptomatic infections, whereas other nonpigmented Bacteroides species were present in acutely infected and asymptomatic teeth with nearly equal frequency. Ultrastructural study of 13 B. buccae strains showed that 8 strains had a crystalline proteinaceous surface layer (S-layer) outside the outer membrane, but all 13 strains had areas of crystalline protein throughout in the outer membrane. The results suggest that B. buccae may have a specific role in the development of an acute opportunistic infection. Images PMID:3782459

  10. 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.

  11. (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.

  12. A Legume TOR Protein Kinase Regulates Rhizobium Symbiosis and Is Essential for Infection and Nodule Development1[OPEN

    PubMed Central

    Blanco, Lourdes; Quinto, Carmen

    2016-01-01

    The target of rapamycin (TOR) protein kinase regulates metabolism, growth, and life span in yeast, animals, and plants in coordination with nutrient status and environmental conditions. The nutrient-dependent nature of TOR functionality makes this kinase a putative regulator of symbiotic associations involving nutrient acquisition. However, TOR’s role in these processes remains to be understood. Here, we uncovered the role of TOR during the bean (Phaseolus vulgaris)-Rhizobium tropici (Rhizobium) symbiotic interaction. TOR was expressed in all tested bean tissues, with higher transcript levels in the root meristems and senesced nodules. We showed TOR promoter expression along the progressing infection thread and in the infected cells of mature nodules. Posttranscriptional gene silencing of TOR using RNA interference (RNAi) showed that this gene is involved in lateral root elongation and root cell organization and also alters the density, size, and number of root hairs. The suppression of TOR transcripts also affected infection thread progression and associated cortical cell divisions, resulting in a drastic reduction of nodule numbers. TOR-RNAi resulted in reduced reactive oxygen species accumulation and altered CyclinD1 and CyclinD3 expression, which are crucial factors for infection thread progression and nodule organogenesis. Enhanced expression of TOR-regulated ATG genes in TOR-RNAi roots suggested that TOR plays a role in the recognition of Rhizobium as a symbiont. Together, these data suggest that TOR plays a vital role in the establishment of root nodule symbiosis in the common bean. PMID:27698253

  13. Rhizobium japonicum mutants defective in symbiotic nitrogen fixation.

    PubMed Central

    Noel, K D; Stacey, G; Tandon, S R; Silver, L E; Brill, W J

    1982-01-01

    Rhizobium japonicum strains 3I1b110 and 61A76 were mutagenized to obtain 25 independently derived mutants that produced soybean nodules defective in nitrogen fixation, as assayed by acetylene reduction. The proteins of both the bacterial and the plant portions of the nodules were analyzed by two-dimensional polyacrylamide gel electrophoresis. All of the mutants had lower-than-normal levels of the nitrogenase components, and all but four contained a prominent bacteroid protein not observed in wild-type bacteroids. Experiments with bacteria grown ex planta suggested that this protein was derepressed by the absence of ammonia. Nitrogenase component II of one mutant was altered in isoelectric point. The soluble plant fraction of the nodules of seven mutants had very low levels of heme, yet the nodules of five of these seven mutants contained the polypeptide of leghemoglobin. Thus, the synthesis of the globin may not be coupled to the content of available heme in soybean nodules. The nodules of the other two of these seven mutants lacked not only leghemoglobin but most of the other normal plant and bacteroid proteins. Ultrastructural examination of nodules formed by these two mutants indicated normal ramification of infection threads but suggested a problem in subsequent survival of the bacteria and their release from the infection threads. Images PMID:6956566

  14. Enhanced expression of Rhizobium etli cbb₃ oxidase improves drought tolerance of common bean symbiotic nitrogen fixation.

    PubMed

    Talbi, C; Sánchez, C; Hidalgo-Garcia, A; González, E M; Arrese-Igor, C; Girard, L; Bedmar, E J; Delgado, M J

    2012-09-01

    To investigate the involvement of Rhizobium etli cbb(3) oxidase in the response of Phaseolus vulgaris to drought, common bean plants were inoculated with the R. etli strain, CFNX713, overexpressing this oxidase in bacteroids (cbb(3)(+)) and subjected to drought conditions. The negative effect of drought on plant and nodule dryweight, nitrogen content, and nodule functionality was more pronounced in plants inoculated with the wild-type (WT) strain than in those inoculated with the cbb(3)(+) strain. Regardless of the plant treatment, bacteroids produced by the cbb(3)(+) strain showed higher respiratory capacity than those produced by the WT strain. Inoculation of plants with the cbb(3)(+) strain alleviated the negative effect of a moderate drought on the respiratory capacity of bacteroids and the energy charge of the nodules. Expression of the FixP and FixO components of the cbb(3) oxidase was higher in bacteroids of the cbb(3)(+) strain than in those of the WT strain under all experimental conditions. The decline in sucrose synthase activity and the decrease in dicarboxylic acids provoked by moderate drought stress were more pronounced in nodules from plants inoculated with the WT strain than in those inoculated with the cbb(3)(+) strain. Taken together, these results suggest that inoculation of plants with a R. etli strain having enhanced expression of cbb(3) oxidase in bacteroids reduces the sensitivity of P. vulgaris-R. etli symbiosis to drought and can modulate carbon metabolism in nodules.

  15. Pyruvate is synthesized by two pathways in pea bacteroids with different efficiencies for nitrogen fixation.

    PubMed

    Mulley, Geraldine; Lopez-Gomez, Miguel; Zhang, Ye; Terpolilli, Jason; Prell, Jurgen; Finan, Turlough; Poole, Philip

    2010-10-01

    Nitrogen fixation in legume bacteroids is energized by the metabolism of dicarboxylic acids, which requires their oxidation to both oxaloacetate and pyruvate. In alfalfa bacteroids, production of pyruvate requires NAD+ malic enzyme (Dme) but not NADP+ malic enzyme (Tme). However, we show that Rhizobium leguminosarum has two pathways for pyruvate formation from dicarboxylates catalyzed by Dme and by the combined activities of phosphoenolpyruvate (PEP) carboxykinase (PckA) and pyruvate kinase (PykA). Both pathways enable N2 fixation, but the PckA/PykA pathway supports N2 fixation at only 60% of that for Dme. Double mutants of dme and pckA/pykA did not fix N2. Furthermore, dme pykA double mutants did not grow on dicarboxylates, showing that they are the only pathways for the production of pyruvate from dicarboxylates normally expressed. PckA is not expressed in alfalfa bacteroids, resulting in an obligate requirement for Dme for pyruvate formation and N2 fixation. When PckA was expressed from a constitutive nptII promoter in alfalfa dme bacteroids, acetylene was reduced at 30% of the wild-type rate, although this level was insufficient to prevent nitrogen starvation. Dme has N-terminal, malic enzyme (Me), and C-terminal phosphotransacetylase (Pta) domains. Deleting the Pta domain increased the peak acetylene reduction rate in 4-week-old pea plants to 140 to 150% of the wild-type rate, and this was accompanied by increased nodule mass. Plants infected with Pta deletion mutants did not have increased dry weight, demonstrating that there is not a sustained change in nitrogen fixation throughout growth. This indicates a complex relationship between pyruvate synthesis in bacteroids, nitrogen fixation, and plant growth.

  16. [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.

  17. Legume-Rhizobium Interactions: Cowpea Root Exudate Elicits Faster Nodulation Response by Rhizobium Species

    PubMed Central

    Bhagwat, Arvind A.; Thomas, Joseph

    1982-01-01

    Preinfection events in legume-Rhizobium symbiosis were analyzed by studying the different nodulation behaviors of two rhizobial strains in cowpeas (Vigna sinensis). Log-phase cultures of Rhizobium sp. strain 1001, an isolate from the plant nodule, initiated host responses leading to infection within 2 h after inoculation, whereas log-phase cultures of Rhizobium sp. strain 32H1 took at least 7 h to trigger a discernible response. The delay observed with strain 32H1 could be eliminated by incubating the rhizobial suspension, before inoculation, for 4.5 h either in the cowpea rhizosphere/rhizoplane condition or in the root exudate of cowpea plants, grown without NH4+ in the rooting medium. The delay could not be eliminated by incubating the rhizobial suspension in the rooting medium of plants grown in the presence of 5 mM NH4+, indicating that there is a regulatory role of combined nitrogen in triggering preinfection events by the legume. The substance(s) in the root exudate which elicited the faster nodulation response by Rhizobium sp. strain 32H1 could be separated into a high-molecular-weight fraction by Sephadex G-100 gel filtration. The data support the notion that legume roots release substances that favor the development of rhizobial features essential for infection and nodulation. PMID:16345989

  18. Development and Partial Characterization of Nearly Isogenic Pea Lines (Pisum sativum L.) that Alter Uptake Hydrogenase Activity in Symbiotic Rhizobium1

    PubMed Central

    Phillips, Donald A.; Kapulnik, Yoram; Bedmar, Eulogio J.; Joseph, Cecillia M.

    1990-01-01

    Some Rhizobium bacteria have H2-uptake (Hup) systems that oxidize H2 evolved from nitrogenase in leguminous root nodules. Pea (Pisum sativum L.) cultivars `JI1205' and `Alaska' produce high Hup (Hup++) and moderate Hup (Hup+) phenotypes, respectively, in Rhizobium leguminosarum 128C53. The physiological significance and biochemical basis of this host plant genetic effect are unknown. The purpose of this investigation was to advance basic Hup studies by developing nearly isogenic lines of peas that alter Hup phenotypes in R. leguminosarum strains containing hup genes. Eight pairs of nearly isogenic pea lines that produce Hup++ and Hup+ phenotypes in R. leguminosarum 128C53 were identified in 173 F2-derived F6 families produced from crosses between JI1205 and Alaska. Tests with the pea isolines and three strains of hup-containing R. leguminosarum showed that the isolines altered Hup activity significantly (P ≤ 0.05) in 19 of 24 symbiotic combinations. Analyses of Hup phenotypes in F6 families, the F1 population, and two backcrosses suggested involvement of a single genetic locus. Three of the eight pairs of isolines were identified as being suitable for physiological studies, because the two lines in each pair showed similar growth, N assimilation, and flowering traits under nonsymbiotic conditions. Tests of those lines under N2-dependent conditions with isogenic Hup+ and negligible Hup (Hup−) mutants of R. leguminosarum 128C53 showed that, in symbioses with Hup+ rhizobia, two out of three Hup++ pea lines decreased N2 fixation relative to Hup+ peas. In one of those cases, however, the Hup++ plant line also decreased fixation by Hup− rhizobia. When results were averaged across all rhizobia tested, Hup+ pea isolines had 8.2% higher dry weight (P ≤ 0.05) and fixed 12.6% more N2 (P ≤ 0.05) than Hup++ isolines. Pea lines described here may help identify host plant factors that influence rhizobial Hup activity and should assist in clarifying how Hup systems

  19. 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

  20. Cefoxitin inactivation by Bacteroides fragilis.

    PubMed

    Cuchural, G J; Tally, F P; Jacobus, N V; Marsh, P K; Mayhew, J W

    1983-12-01

    We have surveyed the susceptibility of 1,575 clinical isolates of the Bacteroides fragilis group of organisms to cefoxitin and eight other antimicrobial agents. Eleven isolates, 0.7% of the total, were highly cefoxitin resistant and had minimum inhibitory concentrations of greater than or equal to 64 micrograms/ml. These isolates were also resistant to other beta-lactam antibiotics. Of 11 isolates, 4 were able to inactivate cefoxitin in broth cultures, as measured by microbiological and high-pressure liquid chromatography assays. Two distinct patterns of cefoxitin breakdown products were detected by high-pressure liquid chromatography analysis. The beta-lactamase inhibitors clavulanic acid and sulbactam failed to show synergism with cefoxitin. These data demonstrate that members of the B. fragilis group have acquired a novel resistance mechanism enabling them to inactivate cefoxitin.

  1. Immunosuppression during Rhizobium-legume symbiosis.

    PubMed

    Luo, Li; Lu, Dawei

    2014-01-01

    Rhizobium infects host legumes to elicit new plant organs, nodules where dinitrogen is fixed as ammonia that can be directly utilized by plants. The nodulation factor (NF) produced by Rhizobium is one of the determinant signals for rhizobial infection and nodule development. Recently, it was found to suppress the innate immunity on host and nonhost plants as well as its analogs, chitins. Therefore, NF can be recognized as a microbe/pathogen-associated molecular pattern (M/PAMP) like chitin to induce the M/PAMP triggered susceptibility (M/PTS) of host plants to rhizobia. Whether the NF signaling pathway is directly associated with the innate immunity is not clear till now. In fact, other MAMPs such as lipopolysaccharide (LPS), exopolysaccharide (EPS) and cyclic-β-glucan, together with type III secretion system (T3SS) effectors are also required for rhizobial infection or survival in leguminous nodule cells. Interestingly, most of them play similarly negative roles in the innate immunity of host plants, though their signaling is not completely elucidated. Taken together, we believe that the local immunosuppression on host plants induced by Rhizobium is essential for the establishment of their symbiosis.

  2. Effective Symbiosis between Rhizobium etli and Phaseolus vulgaris Requires the Alarmone ppGpp

    PubMed Central

    Moris, Martine; Braeken, Kristien; Schoeters, Eric; Verreth, Christel; Beullens, Serge; Vanderleyden, Jos; Michiels, Jan

    2005-01-01

    The symbiotic interaction between Rhizobium etli and Phaseolus vulgaris, the common bean plant, ultimately results in the formation of nitrogen-fixing nodules. Many aspects of the intermediate and late stages of this interaction are still poorly understood. The R. etli relA gene was identified through a genome-wide screening for R. etli symbiotic mutants. RelA has a pivotal role in cellular physiology, as it catalyzes the synthesis of (p)ppGpp, which mediates the stringent response in bacteria. The synthesis of ppGpp was abolished in an R. etli relA mutant strain under conditions of amino acid starvation. Plants nodulated by an R. etli relA mutant had a strongly reduced nitrogen fixation activity (75% reduction). Also, at the microscopic level, bacteroid morphology was altered, with the size of relA mutant bacteroids being increased compared to that of wild-type bacteroids. The expression of the σN-dependent nitrogen fixation genes rpoN2 and iscN was considerably reduced in the relA mutant. In addition, the expression of the relA gene was negatively regulated by RpoN2, the symbiosis-specific σN copy of R. etli. Therefore, an autoregulatory loop controlling the expression of relA and rpoN2 seems operative in bacteroids. The production of long- and short-chain acyl-homoserine-lactones by the cinIR and raiIR systems was decreased in an R. etli relA mutant. Our results suggest that relA may play an important role in the regulation of gene expression in R. etli bacteroids and in the adaptation of bacteroid physiology. PMID:16030240

  3. Acetoacetyl Coenzyme A Reductase and Polyhydroxybutyrate Synthesis in Rhizobium (Cicer) sp. Strain CC 1192

    PubMed Central

    Chohan, Shahid N.; Copeland, Les

    1998-01-01

    Biochemical controls that regulate the biosynthesis of poly-3-hydroxybutyrate (PHB) were investigated in Rhizobium (Cicer) sp. strain CC 1192. This species is of interest for studying PHB synthesis because the polymer accumulates to a large extent in free-living cells but not in bacteroids during nitrogen-fixing symbiosis with chickpea (Cicer arietinum L.) plants. Evidence is presented that indicates that CC 1192 cells retain the enzymic capacity to synthesize PHB when they differentiate from the free-living state to the bacteroid state. This evidence includes the incorporation by CC 1192 bacteroids of radiolabel from [14C]malate into 3-hydroxybutyrate which was derived by chemically degrading insoluble material from bacteroid pellets. Furthermore, the presence of an NADPH-dependent acetoacetyl coenzyme A (CoA) reductase, which was specific for R-(−)-3-hydroxybutyryl-CoA and NADP+ in the oxidative direction, was demonstrated in extracts from free-living and bacteroid cells of CC 1192. Activity of this enzyme in the reductive direction appeared to be regulated at the biochemical level mainly by the availability of substrates. The CC 1192 cells also contained an NADH-specific acetoacetyl-CoA reductase which oxidized S-(+)-3-hydroxybutyryl-CoA. A membrane preparation from CC 1192 bacteroids readily oxidized NADH but not NADPH, which is suggested to be a major source of reductant for nitrogenase. Thus, a high ratio of NADPH to NADP+, which could enhance delivery of reductant to nitrogenase, could also favor the reduction of acetoacetyl-CoA for PHB synthesis. This would mean that fine controls that regulate the partitioning of acetyl-CoA between citrate synthase and 3-ketothiolase are important in determining whether PHB accumulates. PMID:9687441

  4. Introduction of the Escherichia coli gdhA gene into Rhizobium phaseoli: effect on nitrogen fixation.

    PubMed Central

    Bravo, A; Becerril, B; Mora, J

    1988-01-01

    Rhizobium phaseoli lacks glutamate dehydrogenase (GDH) and assimilates ammonium by the glutamine synthetase-glutamate synthase pathway. A strain of R. phaseoli harboring the Escherichia coli GDH structural gene (gdhA) was constructed. GDH activity was expressed in R. phaseoli in the free-living state and in symbiosis. Nodules with bacteroids that expressed GDH activity had severe impairment of nitrogen fixation. Also, R. phaseoli cells that lost GDH activity and assimilated ammonium by the glutamine synthetase-glutamate synthase pathway preferentially nodulated Phaseolus vulgaris. PMID:2892830

  5. Rhizobium pusense is the main human pathogen in the genus Agrobacterium/Rhizobium.

    PubMed

    Aujoulat, F; Marchandin, H; Zorgniotti, I; Masnou, A; Jumas-Bilak, E

    2015-05-01

    Rhizobium pusense was recently described after isolation from the rhizosphere of chickpea. Multilocus sequence-based analysis of clinical isolates identified as Agrobacterium (Rhizobium) radiobacter demonstrated that R. pusense is the main human pathogen within Agrobacterium (Rhizobium) spp. Clinical microbiology of Agrobacterium (Rhizobium) should be considered in the light of recent taxonomic changes.

  6. Bacteroides clarus sp. nov., Bacteroides fluxus sp. nov. and Bacteroides oleiciplenus sp. nov., isolated from human faeces.

    PubMed

    Watanabe, Yohei; Nagai, Fumiko; Morotomi, Masami; Sakon, Hiroshi; Tanaka, Ryuichiro

    2010-08-01

    Three Gram-stain-negative, obligately anaerobic, non-spore-forming, rod-shaped bacteria (strains YIT 12056T, YIT 12057T and YIT 12058T) were isolated from human faeces. These strains were characterized by phylogenetic analyses based on 16S rRNA gene sequence and phenotypic tests. 16S rRNA gene sequence analyses revealed that strains YIT 12056T, YIT 12057T and YIT 12058T were most closely related to the type strains of Bacteroides gallinarum, Bacteroides uniformis and Bacteroides intestinalis with approximate similarity values of 96.6, 95.0 and 96.7%, respectively. The DNA G+C contents of the novel strains were 45.3 (YIT 12056T), 45.2 (YIT 12057T) and 43.6 mol% (YIT 12058T) and the major respiratory quinones of all three isolates were menaquinones MK-10 and MK-11. These properties were typical for members of the genus Bacteroides. The results of the other phenotypic analyses also supported the affiliation of these strains to the genus Bacteroides. The 16S rRNA gene sequence analysis, analysis of the major cellular fatty acids and other biochemical tests enabled the genotypic and phenotypic differentiation of the three new strains. Based on these data, three novel species, Bacteroides clarus sp. nov., Bacteroides fluxus sp. nov. and Bacteroides oleiciplenus sp. nov. are proposed. The type strains of B. clarus, B. fluxus and B. oleiciplenus are YIT 12056T (=JCM 16067T=DSM 22519T), YIT 12057T (=JCM 16101T=DSM 22534T) and YIT 12058T (=JCM 16102T=DSM 22535T), respectively.

  7. 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

  8. Rhizobium etli asparaginase II

    PubMed Central

    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

  9. Identification of feces by detection of Bacteroides genes.

    PubMed

    Nakanishi, Hiroaki; Shojo, Hideki; Ohmori, Takeshi; Hara, Masaaki; Takada, Aya; Adachi, Noboru; Saito, Kazuyuki

    2013-01-01

    In forensic science, the identification of feces is very important in a variety of crime investigations. However, no sensitive and simple fecal identification method using molecular biological techniques has been reported. Here, we focused on the fecal bacteria, Bacteroides uniformis, Bacteroides vulgatus and Bacteroides thetaiotaomicron, and developed a novel fecal identification method by detection of the gene sequences specific to these bacteria in various body (feces, blood, saliva, semen, urine, vaginal fluids and skin surfaces) and forensic (anal adhesions) specimens. Bacterial gene detection was performed by real-time PCR using a minor groove binding probe to amplify the RNA polymerase β-subunit gene of B. uniformis and B. vulgatus, and the α-1-6 mannanase gene of B. thetaiotaomicron. At least one of these bacteria was detected in the feces of 20 donors; the proportions of B. uniformis, B. vulgatus and B. thetaiotaomicron were 95, 85 and 60%, respectively. Bacteroides vulgatus was also detected in one of six vaginal fluid samples, but B. thetaiotaomicron and B. uniformis were not detected in body samples other than feces. Further, we applied this method to forensic specimens from 18 donors. Eighteen anal adhesions also contained at least one of three bacteria; B. uniformis, B. vulgatus and B. thetaiotaomicron were detected in 89, 78 and 56%, respectively, of the specimens. Thus, these bacteria were present at a high frequency in the fecal and forensic specimens, while either B. uniformis or B. vulgatus was detected in all samples. Therefore, B. uniformis and B. vulgatus represent more appropriate target species than B. thetaiotaomicron for the identification of fecal material. If B. vulgatus and/or B. uniformis are detected, it is likely that the sample contains feces. Taken together, our results suggest that the use of molecular biological techniques will aid the detection of feces in forensic practice, although it is possible that the samples contained

  10. 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

  11. Common links in the structure and cellular localization of Rhizobium chitolipooligosaccharides and general Rhizobium membrane phospholipid and glycolipid components.

    PubMed

    Cedergren, R A; Lee, J; Ross, K L; Hollingsworth, R I

    1995-04-04

    Several common links between the structural chemistry of the chitolipooligosaccharides of Rhizobium and the general rhizobial membrane lipid and lipopolysaccharide chemistry of these bacteria have been uncovered. Aspects of common chemistry include sulfation, methylation, and the position and extent of fatty acyl chain unsaturation. We find that bacteria which are known to synthesize sulfated chitolipooligosaccharides (such as Rhizobium meliloti strains and the broad-host-range Rhizobium species strain NGR234) also have sulfated lipopolysaccharides. Their common origins of sulfation have been demonstrated by using mutants which are known to be impaired in sulfating their chitolipooligosaccharides. In such cases, there is a corresponding diminution or complete lack of sulfation of the lipopolysaccharides. The structural diversity of the fatty acids observed in the chitolipooligosaccharides is also observed in the other membrane lipids. For instance, the doubly unsaturated fatty acids which are known to be predominant components of R. meliloti chitolipooligosaccharides were also found in the usual phospholipids and glycolipids. Also, the known functionalization of the chitolipooligosaccharides of R. sp. NGR234 by O- and N-methylation was also reflected in the lipopolysaccharide of this organism. The common structural features of chitolipooligosaccharides and membrane components are consistent with a substantial degree of biosynthetic overlap and a large degree of cellular, spatial overlap between these molecules. The latter aspect is clearly demonstrated here since we show that the chitolipooligosaccharides are, in fact, normal membrane components of Rhizobium. This increases the importance of understanding the role of the bacterial cell surface chemistry in the Rhizobium/legume symbiosis and developing a comprehensive understanding of the highly integrated membrane lipid and glycolipid chemistry of Rhizobium.

  12. 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.

  13. Genetic analysis of the Rhizobium meliloti bacA gene: functional interchangeability with the Escherichia coli sbmA gene and phenotypes of mutants.

    PubMed

    Ichige, A; Walker, G C

    1997-01-01

    The Rhizobium meliloti bacA gene encodes a function that is essential for bacterial differentiation into bacteroids within plant cells in the symbiosis between R. meliloti and alfalfa. An Escherichia coli homolog of BacA, SbmA, is implicated in the uptake of microcin B17, microcin J25 (formerly microcin 25), and bleomycin. When expressed in E. coli with the lacZ promoter, the R. meliloti bacA gene was found to suppress all the known defects of E. coli sbmA mutants, namely, increased resistance to microcin B17, microcin J25, and bleomycin, demonstrating the functional similarity between the two proteins. The R. meliloti bacA386::Tn(pho)A mutant, as well as a newly constructed bacA deletion mutant, was found to show increased resistance to bleomycin. However, it also showed increased resistance to certain aminoglycosides and increased sensitivity to ethanol and detergents, suggesting that the loss of bacA function causes some defect in membrane integrity. The E. coli sbmA gene suppressed all these bacA mutant phenotypes as well as the Fix- phenotype when placed under control of the bacA promoter. Taken together, these results strongly suggest that the BacA and SbmA proteins are functionally similar and thus provide support for our previous hypothesis that BacA may be required for uptake of some compound that plays an important role in bacteroid development. However, the additional phenotypes of bacA mutants identified in this study suggest the alternative possibility that BacA may be needed for membrane integrity, which is likely to be critically important during the early stages of bacterial differentiation within plant cells.

  14. 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

  15. High-resolution transcriptomic analyses of Sinorhizobium sp. NGR234 bacteroids in determinate nodules of Vigna unguiculata and indeterminate nodules of Leucaena leucocephala.

    PubMed

    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.

  16. 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

  17. Iron: an essential micronutrient for the legume-rhizobium symbiosis

    PubMed Central

    Brear, Ella M.; Day, David A.; Smith, Penelope M. C.

    2013-01-01

    Legumes, which develop a symbiosis with nitrogen-fixing bacteria, have an increased demand for iron. Iron is required for the synthesis of iron-containing proteins in the host, including the highly abundant leghemoglobin, and in bacteroids for nitrogenase and cytochromes of the electron transport chain. Deficiencies in iron can affect initiation and development of the nodule. Within root cells, iron is chelated with organic acids such as citrate and nicotianamine and distributed to other parts of the plant. Transport to the nitrogen-fixing bacteroids in infected cells of nodules is more complicated. Formation of the symbiosis results in bacteroids internalized within root cortical cells of the legume where they are surrounded by a plant-derived membrane termed the symbiosome membrane (SM). This membrane forms an interface that regulates nutrient supply to the bacteroid. Consequently, iron must cross this membrane before being supplied to the bacteroid. Iron is transported across the SM as both ferric and ferrous iron. However, uptake of Fe(II) by both the symbiosome and bacteroid is faster than Fe(III) uptake. Members of more than one protein family may be responsible for Fe(II) transport across the SM. The only Fe(II) transporter in nodules characterized to date is GmDMT1 (Glycine max divalent metal transporter 1), which is located on the SM in soybean. Like the root plasma membrane, the SM has ferric iron reductase activity. The protein responsible has not been identified but is predicted to reduce ferric iron accumulated in the symbiosome space prior to uptake by the bacteroid. With the recent publication of a number of legume genomes including Medicago truncatula and G. max, a large number of additional candidate transport proteins have been identified. Members of the NRAMP (natural resistance-associated macrophage protein), YSL (yellow stripe-like), VIT (vacuolar iron transporter), and ZIP (Zrt-, Irt-like protein) transport families show enhanced expression in

  18. Interactions of Bacteroides gingivalis with fibrinogen.

    PubMed Central

    Lantz, M S; Rowland, R W; Switalski, L M; Höök, M

    1986-01-01

    Results of previous studies from our laboratory have shown that a strain of Bacteroides intermedius isolated originally from a patient with acute necrotizing ulcerative gingivitis binds and degrades human fibrinogen (M.S. Lantz, L.M. Switalski, K.S. Kornman, and M. Hook, J. Bacteriol. 163:623-628, 1985). We report that strains of Bacteroides gingivalis, an organism implicated in the etiology of several forms of periodontitis, also bind and degrade fibrinogen. The binding is rapid, reversible, saturable, and specific. The number of fibrinogen-binding sites per cell varies from 500 to 1,500 in different batches of bacteria, and the dissociation constant for the complex is on the order of 10(-8) M. B. gingivalis possesses cell-associated fibrinogenolytic activity that is activated by dithiothreitol and blocked by thiol protease inhibitors. Interaction with fibrinogen may mediate colonization and establishment of these organisms in the periodontal microbiota. Images PMID:3096886

  19. The naringenin-induced exoproteome of Rhizobium etli CE3.

    PubMed

    Meneses, Niurka; Taboada, Hermenegildo; Dunn, Michael F; Vargas, María Del Carmen; Buchs, Natasha; Heller, Manfred; Encarnación, Sergio

    2017-03-02

    Flavonoids excreted by legume roots induce the expression of symbiotically essential nodulation (nod) genes in rhizobia, as well as that of specific protein export systems. In the bean microsymbiont Rhizobium etli CE3, nod genes are induced by the flavonoid naringenin. In this study, we identified 693 proteins in the exoproteome of strain CE3 grown in minimal medium with or without naringenin, with 101 and 100 exoproteins being exclusive to these conditions, respectively. Four hundred ninety-two (71%) of the extracellular proteins were found in both cultures. Of the total exoproteins identified, nearly 35% were also present in the intracellular proteome of R. etli bacteroids, 27% had N-terminal signal sequences and a significant number had previously demonstrated or possible novel roles in symbiosis, including bacterial cell surface modification, adhesins, proteins classified as MAMPs (microbe-associated molecular patterns), such as flagellin and EF-Tu, and several normally cytoplasmic proteins as Ndk and glycolytic enzymes, which are known to have extracellular "moonlighting" roles in bacteria that interact with eukaryotic cells. It is noteworthy that the transmembrane ß (1,2) glucan biosynthesis protein NdvB, an essential symbiotic protein in rhizobia, was found in the R. etli naringenin-induced exoproteome. In addition, potential binding sites for two nod-gene transcriptional regulators (NodD) occurred somewhat more frequently in the promoters of genes encoding naringenin-induced exoproteins in comparison to those ofexoproteins found in the control condition.

  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. 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...

  2. [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.

  3. 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.

  4. Characterization of the urease gene cluster from Rhizobium leguminosarum bv. viciae.

    PubMed

    Toffanin, Annita; Cadahia, Esther; Imperial, Juan; Ruiz-Argüeso, Tomás; Palacios, Manuel

    2002-04-01

    Moderate levels of urease activity (ca. 300 mU mg(-1)) were detected in Rhizobium leguminosarum bv. viciae UPM791 vegetative cells. This activity did not require urea for induction and was partially repressed by the addition of ammonium into the medium. Lower levels of urease activity (ca. 100 mU mg(-1)) were detected also in pea bacteroids. A DNA region of ca. 9 kb containing the urease structural genes ( ureA, ureB and ureC), accessory genes ( ureD, ureE, ureF, and ureG), and five additional ORFs ( orf83, orf135, orf207, orf223, and orf287) encoding proteins of unknown function was sequenced. Three of these ORFs ( orf83, orf135 and orf207) have a homologous counterpart in a gene cluster from Sinorhizobium meliloti, reported to be involved in urease and hydrogenase activities. R. leguminosarum mutant strains carrying Tn 5 insertions within this region exhibited a urease-negative phenotype, but induced wild-type levels of hydrogenase and nitrogenase activities in bacteroids. orf287 encodes a potential transmembrane protein with a C-terminal GGDEF domain. A mutant affected in orf287 exhibited normal levels of urease activity in culture cells. Experiments aimed at cross-complementing Ni-binding proteins required for urease and hydrogenase synthesis (UreE and HypB, respectively) indicated that these two proteins are not functionally interchangeable in R. leguminosarum.

  5. Effect of Plasmid pIJ1008 from Rhizobium leguminosarum on Symbiotic Function of Rhizobium meliloti.

    PubMed

    Bedmar, E J; Brewin, N J; Phillips, D A

    1984-04-01

    Plasmid pIJ1008, which carries determinants for uptake hydrogenase (Hup) activity, was transferred from Rhizobium leguminosarum to Rhizobium meliloti without impairing the capacity of the latter species to form root nodules on alfalfa. The plasmid was still present in rhizobia reisolated from the root nodules of 12 different alfalfa cultivars, but only low levels of Hup activity were detected in alfalfa.

  6. Characterization of Two Inducible Phosphate Transport Systems in Rhizobium tropici

    PubMed Central

    Botero, Lina M.; Al-Niemi, Thamir S.; McDermott, Timothy R.

    2000-01-01

    Rhizobium tropici forms nitrogen-fixing nodules on the roots of the common bean (Phaseolus vulgaris). Like other legume-Rhizobium symbioses, the bean-R. tropici association is sensitive to the availability of phosphate (Pi). To better understand phosphorus movement between the bacteroid and the host plant, Pi transport was characterized in R. tropici. We observed two Pi transport systems, a high-affinity system and a low-affinity system. To facilitate the study of these transport systems, a Tn5B22 transposon mutant lacking expression of the high-affinity transport system was isolated and used to characterize the low-affinity transport system in the absence of the high-affinity system. The Km and Vmax values for the low-affinity system were estimated to be 34 ± 3 μM Pi and 118 ± 8 nmol of Pi · min−1 · mg (dry weight) of cells−1, respectively, and the Km and Vmax values for the high-affinity system were 0.45 ± 0.01 μM Pi and 86 ± 5 nmol of Pi · min−1 · mg (dry weight) of cells−1, respectively. Both systems were inducible by Pi starvation and were also shock sensitive, which indicated that there was a periplasmic binding-protein component. Neither transport system appeared to be sensitive to the proton motive force dissipator carbonyl cyanide m-chlorophenylhydrazone, but Pi transport through both systems was eliminated by the ATPase inhibitor N,N′-dicyclohexylcarbodiimide; the Pi transport rate was correlated with the intracellular ATP concentration. Also, Pi movement through both systems appeared to be unidirectional, as no efflux or exchange was observed with either the wild-type strain or the mutant. These properties suggest that both Pi transport systems are ABC type systems. Analysis of the transposon insertion site revealed that the interrupted gene exhibited a high level of homology with kdpE, which in several bacteria encodes a cytoplasmic response regulator that governs responses to low potassium contents and/or changes in medium

  7. The Rhizobium-plant symbiosis.

    PubMed Central

    van Rhijn, P; Vanderleyden, J

    1995-01-01

    Rhizobium, Bradyrhizobium, and Azorhizobium species are able to elicit the formation of unique structures, called nodules, on the roots or stems of the leguminous host. In these nodules, the rhizobia convert atmospheric N2 into ammonia for the plant. To establish this symbiosis, signals are produced early in the interaction between plant and rhizobia and they elicit discrete responses by the two symbiotic partners. First, transcription of the bacterial nodulation (nod) genes is under control of the NodD regulatory protein, which is activated by specific plant signals, flavonoids, present in the root exudates. In return, the nod-encoded enzymes are involved in the synthesis and excretion of specific lipooligosaccharides, which are able to trigger on the host plant the organogenic program leading to the formation of nodules. An overview of the organization, regulation, and function of the nod genes and their participation in the determination of the host specificity is presented. PMID:7708010

  8. Development of Bacteroides 16S rRNA Gene TaqMan-Based Real-Time PCR Assays for Estimation of Total, Human, and Bovine Fecal Pollution in Water

    PubMed Central

    Layton, Alice; McKay, Larry; Williams, Dan; Garrett, Victoria; Gentry, Randall; Sayler, Gary

    2006-01-01

    Bacteroides species are promising indicators for differentiating livestock and human fecal contamination in water because of their high concentration in feces and potential host specificity. In this study, a real-time PCR assay was designed to target Bacteroides species (AllBac) present in human, cattle, and equine feces. Direct PCR amplification (without DNA extraction) using the AllBac assay was tested on feces diluted in water. Fecal concentrations and threshold cycle were linearly correlated, indicating that the AllBac assay can be used to estimate the total amount of fecal contamination in water. Real-time PCR assays were also designed for bovine-associated (BoBac) and human-associated (HuBac) Bacteroides 16S rRNA genes. Assay specificities were tested using human, bovine, swine, canine, and equine fecal samples. The BoBac assay was specific for bovine fecal samples (100% true-positive identification; 0% false-positive identification). The HuBac assay had a 100% true-positive identification, but it also had a 32% false-positive rate with potential for cross-amplification with swine feces. The assays were tested using creek water samples from three different watersheds. Creek water did not inhibit PCR, and results from the AllBac assay were correlated with those from Escherichia coli concentrations (r2 = 0.85). The percentage of feces attributable to bovine and human sources was determined for each sample by comparing the values obtained from the BoBac and HuBac assays with that from the AllBac assay. These results suggest that real-time PCR assays without DNA extraction can be used to quantify fecal concentrations and provide preliminary fecal source identification in watersheds. PMID:16751534

  9. Development of a Real-Time PCR Assay for Detection and Quantification of Rhizobium leguminosarum Bacteria and Discrimination between Different Biovars in Zinc-Contaminated Soil▿

    PubMed Central

    Macdonald, Catriona A.; Clark, Ian M.; Hirsch, Penny R.; Zhao, Fang-Jie; McGrath, Steve P.

    2011-01-01

    Primers were designed to target 16S rRNA and nodD genes of Rhizobium leguminosarum from DNA extracted from two different soil types contaminated with Zn applied in sewage sludge. Numbers of rhizobia estimated using 16S rRNA gene copy number showed higher abundance than those estimated by both nodD and the most-probable-number (MPN) enumeration method using a plant trap host. Both 16S rRNA gene copies and the MPN rhizobia declined with increased levels of Zn contamination, as did the abundance of the functional gene nodD, providing compelling evidence of a toxic effect of Zn on R. leguminosarum populations in the soil. Regression analysis suggested the total Zn concentration in soil as a better predictor of rhizobial numbers than both NH4NO3-extractable and soil solution Zn. R. leguminosarum bv. viciae nodD gene copies were generally less sensitive to Zn than R. leguminosarum bv. trifolii nodD. The latter were generally below detection limits at Zn levels of >250 mg kg−1. Although there were differences in the actual numbers estimated by each approach, the response to Zn was broadly similar across all methods. These differences were likely to result from the fact that the molecular approaches assess the potential for nodulation while the MPN approach assesses actual nodulation. The results demonstrate that the use of targeted gene probes for assessing environmental perturbations of indigenous soil rhizobial populations may be more sensitive than the conventional plant bioassay and MPN methods. PMID:21602380

  10. Patient-Specific Bacteroides Genome Variants in Pouchitis

    PubMed Central

    Vineis, Joseph H.; Ringus, Daina L.; Morrison, Hilary G.; Delmont, Tom O.; Dalal, Sushila; Raffals, Laura H.; Antonopoulos, Dionysios A.; Rubin, David T.; Eren, A. Murat; Chang, Eugene B.

    2016-01-01

    ABSTRACT A 2-year longitudinal microbiome study of 22 patients who underwent colectomy with an ileal pouch anal anastomosis detected significant increases in distinct populations of Bacteroides during 9 of 11 patient visits that coincided with inflammation (pouchitis). Oligotyping and metagenomic short-read annotation identified Bacteroides populations that occurred in early samples, bloomed during inflammation, and reappeared after antibiotic treatment. Targeted cultivation of Bacteroides isolates from the same individual at multiple time points and from several patients detected subtle genomic changes, including the identification of rapidly evolving genomic elements that differentiate isogenic strains of Bacteroides fragilis from the mucosa versus lumen. Each patient harbored Bacteroides spp. that are closely related to commonly occurring clinical isolates, including Bacteroides ovatus, B. thetaiotaomicron, B. vulgatus, and B. fragilis, which contained unique loci in different patients for synthesis of capsular polysaccharides. The presence of unique Bacteroides capsular polysaccharide loci within different hosts and between the lumen and mucosa may represent adaptations to stimulate, suppress, and evade host-specific immune responses at different microsites of the ileal pouch. PMID:27935837

  11. Cellular immunity to Bacteroides fragilis capsular polysaccharide

    PubMed Central

    1982-01-01

    The polysaccharide capsule of Bacteroides fragilis has been shown to be important in the virulence of the organism. The capsular polysaccharide (CP) of B. fragilis has been extensively purified. Using a murine model of intraabdominal abscess formation, we have been able to demonstrate cellular immunity to the capsular polysaccharide of B. fragilis. Immunization of C57BL/10J mice with the CP over 5 wk prevents abscess formation when the mice are challenged with B. fragilis intraperitoneally. This immunity can be transferred to naive mice with spleen cells from immune animals. The immune cells bear Thy-1.2 and Ly- 2.2 antigens. The immune response has been shown to be antigen specific, but not H-2 restricted. The possibility that these immune cells are suppressor T cells is discussed. The experimental system presented provides a model for the examination of the cellular interactions responsible for abscess formation and the cellular response to bacterial pathogens. PMID:6174672

  12. [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

  13. Strain identification and quorum sensing inhibition characterization of marine-derived Rhizobium sp. NAO1

    PubMed Central

    Chang, Hong; Zhu, Xiaoshan; Yu, Shenchen; Chen, Lu; Jin, Hui; Cai, Zhonghua

    2017-01-01

    A novel strategy for combating pathogens is through the ongoing development and use of anti-quorum sensing (QS) treatments such as therapeutic bacteria or their anti-QS substances. Relatively little is known about the bacteria that inhabit the open ocean and of their potential anti-pathogenic attributes; thus, in an initiative to identify these types of therapeutic bacteria, planktonic microbes from the North Atlantic Ocean were collected, isolated, cultured and screened for anti-QS activity. Screening analysis identified one such strain, Rhizobium sp. NAO1. Extracts of Rhizobium sp. NAO1 were identified via ultra-performance liquid chromatography (UPLC) analysis. They were shown to contain N-acyl homoserine lactone (AHL)-based QS analogues (in particular, the N-butyryl homoserine lactone (C4-AHL) analogue) and could disrupt biofilm formation by Pseudomonas aeruginosa PAO1. QS inhibition was confirmed using confocal scanning laser microscopy and growth curves, and it was shown to occur in a dose-dependent manner without affecting bacterial growth. Secondary metabolites of Rhizobium sp. NAO1 inhibited PAO1 pathogenicity by downregulating AHL-mediated virulence factors such as elastase activity and siderophore production. Furthermore, as a result of biofilm structure damage, the secondary metabolite products of Rhizobium sp. NAO1 significantly increased the sensitivity of PAO1 to aminoglycoside antibiotics. Our results demonstrated that Rhizobium sp. strain NAO1 has the ability to disrupt P. aeruginosa PAO1 biofilm architecture, in addition to attenuating P. aeruginosa PAO1 virulence factor production and pathogenicity. Therefore, the newly identified ocean-derived Rhizobium sp. NAO1 has the potential to serve as a QS inhibitor and may be a new microbial resource for drug development.

  14. Effect of Plasmid pIJ1008 from Rhizobium leguminosarum on Symbiotic Function of Rhizobium meliloti

    PubMed Central

    Bedmar, E. J.; Brewin, N. J.; Phillips, D. A.

    1984-01-01

    Plasmid pIJ1008, which carries determinants for uptake hydrogenase (Hup) activity, was transferred from Rhizobium leguminosarum to Rhizobium meliloti without impairing the capacity of the latter species to form root nodules on alfalfa. The plasmid was still present in rhizobia reisolated from the root nodules of 12 different alfalfa cultivars, but only low levels of Hup activity were detected in alfalfa. PMID:16346527

  15. 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)).

  16. Autotransmissible resident plasmid of Rhizobium meliloti.

    PubMed

    Bedmar, E J; Olivares, J

    1980-01-01

    A resident plasmid of wild-type strains of Rhizobium meliloti of 59.6 megadaltons has been shown to be transferred at a high frequency to "cured" strains of this bacterial species. This plasmid, named pEZ1, that confers phage-sensitivity to cells carrying it is also transmissible to Escherichia coli and from it to "cured" R. meliloti strains.

  17. Two Sinorhizobium meliloti glutaredoxins regulate iron metabolism and symbiotic bacteroid differentiation.

    PubMed

    Benyamina, Sofiane M; Baldacci-Cresp, Fabien; Couturier, Jérémy; Chibani, Kamel; Hopkins, Julie; Bekki, Abdelkader; de Lajudie, Philippe; Rouhier, Nicolas; Jacquot, Jean-Pierre; Alloing, Geneviève; Puppo, Alain; Frendo, Pierre

    2013-03-01

    Legumes interact symbiotically with bacteria of the Rhizobiaceae to form nitrogen-fixing root nodules. We investigated the contribution of the three glutaredoxin (Grx)-encoding genes present in the Sinorhizobium meliloti genome to this symbiosis. SmGRX1 (CGYC active site) and SmGRX3 (CPYG) recombinant proteins displayed deglutathionylation activity in the 2-hydroethyldisulfide assay, whereas SmGRX2 (CGFS) did not. Mutation of SmGRX3 did not affect S. meliloti growth or symbiotic capacities. In contrast, SmGRX1 and SmGRX2 mutations decreased the growth of free-living bacteria and the nitrogen fixation capacity of bacteroids. Mutation of SmGRX1 led to nodule abortion and an absence of bacteroid differentiation, whereas SmGRX2 mutation decreased nodule development without modifying bacteroid development. The higher sensitivity of the Smgrx1 mutant strain as compared with wild-type strain to oxidative stress was associated with larger amounts of glutathionylated proteins. The Smgrx2 mutant strain displayed significantly lower levels of activity than the wild type for two iron-sulfur-containing enzymes, aconitase and succinate dehydrogenase. This lower level of activity could be associated with deregulation of the transcriptional activity of the RirA iron regulator and higher intracellular iron content. Thus, two S. meliloti Grx proteins are essential for symbiotic nitrogen fixation, playing independent roles in bacterial differentiation and the regulation of iron metabolism.

  18. 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.

  19. A Transmissible Plant Shoot Factor Promotes Uptake Hydrogenase Activity in Rhizobium Symbionts 1

    PubMed Central

    Bedmar, Eulogio J.; Phillips, Donald A.

    1984-01-01

    Shoot/root grafting studies showed organ and host cultivar effects on net H2 evolution from Pisum sativum L. root nodules. Net H2 evolution from those nodules represents the sum of H2 formed by Rhizobium nitrogenase and H2 oxidized by any uptake hydrogenase present in the bacteria. Grafts between pea cultivars `JI1205' or `Alaska' and `Feltham First' in symbioses with R. leguminosarum 128C53 showed that shoots of both JI1205 and Alaska increased H2 uptake significantly (P ≤ 0.05) in Feltham First root nodules. The same plants also had less net H2 evolution at similar rates of C2H2 reduction than plants formed by grafting Feltham First shoots on Feltham First roots. Although JI1205 and Alaska shoots increased H2-uptake activity of Feltham First root nodules 28 days after the graft was made, intermediate to high levels of H2 uptake activity were still present in nodules on roots of both JI1205 and Alaska grafted to Feltham First shoots. These results indicate the presence of a transmissible shoot factor(s) which can increase uptake hydrogenase activity in a Rhizobium symbiont and show that root genotype also can influence that parameter. Parallel grafting experiments using the same pea cultivars in symbioses with R. leguminosarum strain 300, which lacks uptake hydrogenase activity, suggested that a transmissible shoot factor(s) altered H2 formation from nitrogenase by changing the electron allocation coefficient of that enzyme complex. The root and shoot factor(s) detected in this study had no permanent effect on strain 128C53. Bacterial cells isolated from Feltham First nodules with low H2 uptake activity formed root nodules on JI1205 and Alaska with high H2 uptake activity. Bacteroids isolated from nodules on intact JI1205, Alaska, or Feltham First plants with high, medium, or low H2 uptake activity, respectively, maintained those phenotypes during in vitro assays. PMID:16663677

  20. A transmissible plant shoot factor promotes uptake hydrogenase activity in Rhizobium symbionts.

    PubMed

    Bedmar, E J; Phillips, D A

    1984-07-01

    Shoot/root grafting studies showed organ and host cultivar effects on net H(2) evolution from Pisum sativum L. root nodules. Net H(2) evolution from those nodules represents the sum of H(2) formed by Rhizobium nitrogenase and H(2) oxidized by any uptake hydrogenase present in the bacteria. Grafts between pea cultivars ;JI1205' or ;Alaska' and ;Feltham First' in symbioses with R. leguminosarum 128C53 showed that shoots of both JI1205 and Alaska increased H(2) uptake significantly (P Rhizobium symbiont and show that root genotype also can influence that parameter.Parallel grafting experiments using the same pea cultivars in symbioses with R. leguminosarum strain 300, which lacks uptake hydrogenase activity, suggested that a transmissible shoot factor(s) altered H(2) formation from nitrogenase by changing the electron allocation coefficient of that enzyme complex.The root and shoot factor(s) detected in this study had no permanent effect on strain 128C53. Bacterial cells isolated from Feltham First nodules with low H(2) uptake activity formed root nodules on JI1205 and Alaska with high H(2) uptake activity. Bacteroids isolated from nodules on intact JI1205, Alaska, or Feltham First plants with high, medium, or low H(2) uptake activity, respectively, maintained those phenotypes during in vitro assays.

  1. Decreased susceptibility to nitroimidazoles among Bacteroides species in Brazil.

    PubMed

    B D Vieira, Jessica Manya; Boente, Renata F; Rodrigues Miranda, Karla; Avelar, Kátia E S; M C P Domingues, Regina; Candida de S Ferreira, Maria

    2006-01-01

    In this study, 197 strains of Bacteroides genus from different species and origins were evaluated with regard to their susceptibility to 5-nitroimidazoles (5-Ni)-such as tinidazole, ornidazole, and metronidazole-using the agar dilution method. The presence of nim genes was also investigated by polymerase chain reaction. It was found that 5.6% of Bacteroides strains among all origins showed decreased susceptibility (minimum inhibitory concentrations varying from 4 to 16 microg/ml) to at least one of the imidazoles studied without any known nim gene associate. Also, we detected one strain isolated from a polluted aquatic environment in which one nim gene was found and characterized as nim B using restriction fragment length polymorphism and sequencing. Hence, resistance to 5-Ni should be monitored closely because they constitute, among few drugs, the ones quite effective in treating Bacteroides infections.

  2. Conserved Plasmid Hydrogen-Uptake (hup)-Specific Sequences within Hup+Rhizobium leguminosarum Strains

    PubMed Central

    Leyva, Antonio; Palacios, José M.; Ruiz-Argüeso, Tomás

    1987-01-01

    Thirteen Rhizobium leguminosarum strains previously reported as H2-uptake hydrogenase positive (Hup+) or negative (Hup−) were analyzed for the presence and conservation of DNA sequences homologous to cloned Bradyrhizobium japonicum hup-specific DNA from cosmid pHU1 (M. A. Cantrell, R. A. Haugland, and H. J. Evans, Proc. Natl. Acad. Sci. USA 80:181-185, 1983). The Hup phenotype of these strains was reexamined by determining hydrogenase activity induced in bacteroids from pea nodules. Five strains, including H2 oxidation-ATP synthesis-coupled and -uncoupled strains, induced significant rates of H2-uptake hydrogenase activity and contained DNA sequences homologous to three probe DNA fragments (5.9-kilobase [kb] HindIII, 2.9-kb EcoRI, and 5.0-kb EcoRI) from pHU1. The pattern of genomic DNA HindIII and EcoRI fragments with significant homology to each of the three probes was identical in all five strains regardless of the H2-dependent ATP generation trait. The restriction fragments containing the homology totalled about 22 kb of DNA common to the five strains. In all instances the putative hup sequences were located on a plasmid that also contained nif genes. The molecular sizes of the identified hup-sym plasmids ranged between 184 and 212 megadaltons. No common DNA sequences homologous to B. japonicum hup DNA were found in genomic DNA from any of the eight remaining strains showing no significant hydrogenase activity in pea bacteroids. These results suggest that the identified DNA region contains genes essential for hydrogenase activity in R. leguminosarum and that its organization is highly conserved within Hup+ strains in this symbiotic species. Images PMID:16347471

  3. Rhizobium japonicum mutants that are hypersensitive to repression of H2 uptake by oxygen.

    PubMed

    Maier, R J; Merberg, D M

    1982-04-01

    The synthesis of an H2 oxidation system in free-living Rhizobium japonicum wild-type strain SR is repressed by oxygen. Maximal H2 uptake rates were obtained in strain SR after derepression in 11 microM or less dissolved oxygen. Oxygen levels above 45 microM completely repressed H2 uptake in strain SR. Five R. japonicum mutant strains that are hypersensitive to repression or H2 oxidation by oxygen were derived from strain SR. The mutants were obtained by screening H2 uptake-negative mutants that retained the ability to oxidize H2 as bacteroids from soybean nodules. As bacteroids, the five mutant strains were capable of H2 oxidation rates comparable to that of the wild type. The mutants did not take up H2 when derepressed in 22 microM dissolved oxygen, whereas strain SR had substantial activity at this oxygen concentration. The O2 repression of H2 uptake in both the wild-type and two mutant strains, SR174 and SR200, was rapid and was similar to the effect of inhibiting synthesis of H2 uptake system components with rifampin. None of the mutant strains was able to oxidize H2 when the artificial electron acceptors methylene blue or phenazine methosulfate were provided. The mutant strains were not sensitive to killing by oxygen, they took up O2 at rates similar to strain SR, and they did not produce an H2 uptake system that was oxygen labile. Cyclic AMP levels were comparable in strain SR and the five mutant strains after subjection of the cultures to the derepression conditions.

  4. Rhizobium japonicum mutants that are hypersensitive to repression of H2 uptake by oxygen.

    PubMed Central

    Maier, R J; Merberg, D M

    1982-01-01

    The synthesis of an H2 oxidation system in free-living Rhizobium japonicum wild-type strain SR is repressed by oxygen. Maximal H2 uptake rates were obtained in strain SR after derepression in 11 microM or less dissolved oxygen. Oxygen levels above 45 microM completely repressed H2 uptake in strain SR. Five R. japonicum mutant strains that are hypersensitive to repression or H2 oxidation by oxygen were derived from strain SR. The mutants were obtained by screening H2 uptake-negative mutants that retained the ability to oxidize H2 as bacteroids from soybean nodules. As bacteroids, the five mutant strains were capable of H2 oxidation rates comparable to that of the wild type. The mutants did not take up H2 when derepressed in 22 microM dissolved oxygen, whereas strain SR had substantial activity at this oxygen concentration. The O2 repression of H2 uptake in both the wild-type and two mutant strains, SR174 and SR200, was rapid and was similar to the effect of inhibiting synthesis of H2 uptake system components with rifampin. None of the mutant strains was able to oxidize H2 when the artificial electron acceptors methylene blue or phenazine methosulfate were provided. The mutant strains were not sensitive to killing by oxygen, they took up O2 at rates similar to strain SR, and they did not produce an H2 uptake system that was oxygen labile. Cyclic AMP levels were comparable in strain SR and the five mutant strains after subjection of the cultures to the derepression conditions. PMID:6277861

  5. RbohB, a Phaseolus vulgaris NADPH oxidase gene, enhances symbiosome number, bacteroid size, and nitrogen fixation in nodules and impairs mycorrhizal colonization.

    PubMed

    Arthikala, Manoj-Kumar; Sánchez-López, Rosana; Nava, Noreide; Santana, Olivia; Cárdenas, Luis; Quinto, Carmen

    2014-05-01

    The reactive oxygen species (ROS) generated by respiratory burst oxidative homologs (Rbohs) are involved in numerous plant cell signaling processes, and have critical roles in the symbiosis between legumes and nitrogen-fixing bacteria. Previously, down-regulation of RbohB in Phaseolus vulgaris was shown to suppress ROS production and abolish Rhizobium infection thread (IT) progression, but also to enhance arbuscular mycorrhizal fungal (AMF) colonization. Thus, Rbohs function both as positive and negative regulators. Here, we assessed the effect of enhancing ROS concentrations, by overexpressing PvRbohB, on the P. vulgaris--rhizobia and P. vulgaris--AMF symbioses. We estimated superoxide concentrations in hairy roots overexpressing PvRbohB, determined the status of early and late events of both Rhizobium and AMF interactions in symbiont-inoculated roots, and analyzed the nodule ultrastructure of transgenic plants overexpressing PvRbohB. Overexpression of PvRbohB significantly enhanced ROS production, the formation of ITs, nodule biomass, and nitrogen-fixing activity, and increased the density of symbiosomes in nodules, and the density and size of bacteroides in symbiosomes. Furthermore, PvCAT, early nodulin, PvSS1, and PvGOGAT transcript abundances were elevated in these nodules. By contrast, mycorrhizal colonization was reduced in roots that overexpressed RbohB. Overexpression of PvRbohB augmented nodule efficiency by enhancing nitrogen fixation and delaying nodule senescence, but impaired AMF colonization.

  6. Occurrence of polyamines in root nodules of Phaseolus vulgaris in symbiosis with Rhizobium tropici in response to salt stress.

    PubMed

    López-Gómez, Miguel; Cobos-Porras, Libertad; Hidalgo-Castellanos, Javier; Lluch, Carmen

    2014-11-01

    Polyamines (PAs) are low molecular weight aliphatic compounds that have been shown to be an important part of plant responses to salt stress. For that reason in this work we have investigated the involvement of PAs in the response to salt stress in root nodules of Phaseolus vulgaris in symbiosis with Rhizobium tropici. The level and variety of PAs was higher in nodules, compared to leaves and roots, and in addition to the common PAs (putrescine, spermidine and spermine) we found homospermidine (Homspd) as the most abundant polyamine in nodules. UPLC-mass spectrometry analysis revealed the presence of 4-aminobutylcadaverine (4-ABcad), only described in nodules of Vigna angularis before. Indeed, the analysis of different nodular fractions revealed higher level of 4-ABcad, as well as Homspd, in bacteroids which indicate the production of these PAs by the bacteria in symbiosis. The genes involved in PAs biosynthesis in nodules displayed an induction under salt stress conditions which was not consistent with the decline of free PAs levels, probably due to the nitrogen limitations provoked by the nitrogenase activity depletion and/or the conversion of free PAs to theirs soluble conjugated forms, that seems to be one of the mechanisms involved in the regulation of PAs levels. On the contrary, cadaverine (Cad) and 4-ABcad concentrations augmented by the salinity, which might be due to their involvement in the response of bacteroids to hyper-osmotic conditions. In conclusion, the results shown in this work suggest the alteration of the bacteroidal metabolism towards the production of uncommon PAs such as 4-ABcad in the response to salt stress in legume root nodules.

  7. Chromosomal DNA probes for the identification of Bacteroides tectum and Bacteroides fragilis from the oral cavity of cats.

    PubMed

    Love, D N; Bailey, G D

    1993-01-01

    A dot-blot hybridisation assay using high molecular weight DNA as whole chromosomal probes was used to differentiate Bacteroides tectum from Bacteroides fragilis. 32P-labelled probes were compared with digoxigenin (DIG)-labelled probes. The whole chromosomal probes were specific--differentiating B. tectum from B. fragilis and both from a variety of other species (including other members of the genera Bacteroides, Fusobacterium, Eubacterium, and Prevotella) found in normal and abnormal mouths of cats and horses. However, even at very high stringencies, B. tectum homology groups I, II and III were not distinguishable from one another using either 32P-labelled or DIG-labelled probes. Thus, DIG-labelled whole chromosome probes directed against cellular DNA released directly onto nitrocellulose membranes is considered a useful method for diagnostic veterinary laboratories wishing to identify B. tectum and distinguish it from B. fragilis and other oral anaerobic flora of cats.

  8. Evolutionary origin of rhizobium Nod factor signaling

    PubMed Central

    Streng, Arend; op den Camp, Rik; Bisseling, Ton

    2011-01-01

    For over two decades now, it is known that the nodule symbiosis between legume plants and nitrogen fixing rhizobium bacteria is set in motion by the bacterial signal molecule named nodulation (Nod) factor.1 Upon Nod factor perception a signaling cascade is activated that is also essential for endomycorrhizal symbiosis (Fig. 1). This suggests that rhizobium co-opted the evolutionary far more ancient mycorrhizal signaling pathway in order to establish an endosymbiotic interaction with legumes.2 As arbuscular mycorrhizal fungi of the Glomeromycota phylum can establish a symbiosis with the vast majority of land plants, it is most probable that this signaling cascade is wide spread in the plant kingdom.3 However, Nod factor perception generally is considered to be unique to legumes. Two recent breakthroughs on the evolutionary origin of rhizobium Nod factor signaling demonstrate that this is not the case.4,5 The purification of Nod factor-like molecules excreted by the mycorrhizal fungus Glomus intraradices and the role of the LysM-type Nod factor receptor PaNFP in the non-legume Parasponia andersonii provide novel understanding on the evolution of rhizobial Nod factor signaling. PMID:21904113

  9. Detection of Bacteroides fragilis, Bacteroides thetaiotaomicron, and Bacteroides ovatus in clinical specimens by immunofluorescence with a monoclonal antibody to B. fragilis lipopolysaccharide.

    PubMed Central

    Viljanen, M K; Linko, L; Lehtonen, O P

    1988-01-01

    A total of 1,897 clinical specimens (1,019 aspirates and 876 swabs) were studied by indirect immunofluorescence (IF) with a mouse monoclonal antibody (MAb) against a D-galactose oligomer of Bacteroides fragilis lipopolysaccharide. The MAb has been shown to react with 96% of clinical B. fragilis isolates and with about 50% of Bacteroides ovatus and Bacteroides thetaiotaomicron isolates but not with other aerobic or anaerobic organisms tested. The sensitivity of IF in comparison with culturing was 78.9% for all three species. Of the 32 strains originating from culture-positive, IF-negative specimens, 13 lacked the target determinant for the MAb. Sensitivity was highest with specimens taken from the perineal area (87.1%) and lowest with those taken from undefined sites (56.6%). Sensitivity was better with aspirates (86.8%) than with swabs (72.6%). The specificity of IF was 95.6% for all of the material. Positive and negative predictive values were 51.1 and 98.0%, respectively. Neither long transportation times of specimens nor antimicrobial therapy seemed to correlate with the occurrence of IF-positive, culture-negative specimens. This study shows that a single MAb can be used to establish an IF assay that can complement isolation in the detection of these three members of the B. fragilis group. Images PMID:3281973

  10. 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...

  11. Putative porin of Bradyrhizobium sp. (Lupinus) bacteroids induced by glyphosate.

    PubMed

    de María, Nuria; Guevara, Angeles; Serra, M Teresa; García-Luque, Isabel; González-Sama, Alfonso; García de Lacoba, Mario; de Felipe, M Rosario; Fernández-Pascual, Mercedes

    2007-08-01

    Application of glyphosate (N-[phosphonomethyl] glycine) to Bradyrhizobium sp. (Lupinus)-nodulated lupin plants caused modifications in the protein pattern of bacteroids. The most significant change was the presence of a 44-kDa polypeptide in bacteroids from plants treated with the higher doses of glyphosate employed (5 and 10 mM). The polypeptide has been characterized by the amino acid sequencing of its N terminus and the isolation and nucleic acid sequencing of its encoding gene. It is putatively encoded by a single gene, and the protein has been identified as a putative porin. Protein modeling revealed the existence of several domains sharing similarity to different porins, such as a transmembrane beta-barrel. The protein has been designated BLpp, for Bradyrhizobium sp. (Lupinus) putative porin, and would be the first porin described in Bradyrhizobium sp. (Lupinus). In addition, a putative conserved domain of porins has been identified which consists of 87 amino acids, located in the BLpp sequence 30 amino acids downstream of the N-terminal region. In bacteroids, mRNA of the BLpp gene shows a basal constitutive expression that increases under glyphosate treatment, and the expression of the gene is seemingly regulated at the transcriptional level. By contrast, in free-living bacteria glyphosate treatment leads to an inhibition of BLpp mRNA accumulation, indicating a different effect of glyphosate on BLpp gene expression in bacteroids and free-living bacteria. The possible role of BLpp in a metabolite interchange between Bradyrhizobium and lupin is discussed.

  12. Characteristics of bacteroids in indeterminate nodules of the leguminous tree Leucaena glauca.

    PubMed

    Ishihara, Hironobu; Koriyama, Hiroki; Osawa, Atsushi; Zehirov, Grigor; Yamaura, Masatoshi; Kucho, Ken-ichi; Abe, Mikiko; Higashi, Shiro; Kondorosi, Eva; Mergaert, Peter; Uchiumi, Toshiki

    2011-01-01

    Rhizobia establish symbiosis with legumes. Bacteroids in indeterminate nodules of Inverted Repeat Lacking Clade (IRLC) legumes undergo terminal differentiation caused by Nodule-specific Cysteine-Rich peptides (NCRs). Microscopic observations of bacteroids and the detection of NCRs in indeterminate nodules of the non-IRLC legume Leucaena glauca were performed. A portion of the bacteroids showed moderate cell elongation, loss of membrane integrity, and multiple nucleoids. The symbiosome contained multiple bacteroids and NCR-like peptides were not detectable. These results indicate that bacteroid differentiation in L. glauca is different from that in IRLC legumes although both hosts form indeterminate nodules.

  13. Control of ammonium assimilation in Rhizobium 32H1.

    PubMed Central

    Ludwig, R A

    1978-01-01

    The symbiotic, nitrogen-fixing bacterium Rhizobium sp. 32H1 is a specialized ammonium producer during symbiosis. However, during free-living growth, Rhizobium 32H1 assimilates ammonium very poorly. Two pathways of ammonium assimilation exist in enteric bacteria. One is mediated by glutamate dehydrogenase, and the other is mediated by glutamine synthetase-glutamate synthase. The former pathway is altogether inoperative in Rhizobium 32H1; the latter pathway operates at a slow rate and is under strict negative control by ammonium itself. Rhizobium 32H1 glutamine synthetase activity is modulated by both repression-derepression and reversible adenylylation. For a biochemical process lacking an alternative pathway, such a regulatory pattern exacerbates the very process. This suggests that Rhizobium 32H1 restricts its own ammonium assimilation to maximize the contribution of fixed nitrogen to the host plant during symbiosis. PMID:27498

  14. Role of GOGAT in carbon and nitrogen partitioning in Rhizobium etli.

    PubMed

    Castillo, A; Taboada, H; Mendoza, A; Valderrama, B; Encarnación, S; Mora, J

    2000-07-01

    The isolation and characterization of a Rhizobium etli glutamate auxotroph, TAD12, harbouring a single Tn5 insertion, is reported. This mutant produced no detectable glutamate synthase (GOGAT) activity. The cloning and physical characterization of a 7.2 kb fragment of R. etli DNA harbouring the structural genes gltB and gltD encoding the two GOGAT subunits GltB and GltD is also reported. In comparison with the wild-type strain (CFN42), the GOGAT mutant strain utilized less succinate and glutamate and grew less with this and other amino acids as nitrogen source. R. etli assimilates ammonium by the glutamine synthetase (GS)-GOGAT pathway and a GOGAT mutant prevents the cycling of glutamine by this pathway, something that impairs nitrogen and carbon metabolism and explains the decrease in the amino-nitrogen during exponential growth, with glutamate as nitrogen source. GOGAT activity also has a role in ammonium turnover and in the synthesis of amino acids and proteins, processes that are necessary to sustain cell viability in non-growing conditions. The assimilation of ammonium is important during symbiosis and glutamate constitutes 20-40% of the total amino-nitrogen. In symbiosis, the blockage of ammonium assimilation by a GOGAT mutation significantly decreases the amino-nitrogen pool of the bacteroids and may explain why more N(2) is fixed in ammonium, excreted to the plant cell, transported to the leaves and stored in the seeds.

  15. Synergism between Penicillin, Clindamycin, or Metronidazole and Gentamicin against Species of the Bacteroides melaninogenicus and Bacteroides fragilis Groups

    DTIC Science & Technology

    1984-01-01

    with other antibiotics, such as clinda- In this study. 30 strains of Bacreroides spp. were tested for mycin (4. 18) and spiramycin (111). which proved to...BACTEROIDES SPP. 77 This work was supported in panr by grant 68011 from the Upjohn -netronidazole- spiramycine : conlcenltrationls et syflergic in situ Co

  16. Rhizobium halotolerans sp. nov., Isolated from chloroethylenes contaminated soil.

    PubMed

    Diange, Eboa Adolf; Lee, Sang-Seob

    2013-06-01

    The strain designated as AB21(T) was isolated from chloroethylenes contaminated soil. Cells are gram-negative, aerobic, non-spore-forming, and motile rods. Phylogenetic analysis based on 16S rRNA gene sequence showed that it belonged to the genus Rhizobium, and was closely related to Rhizobium sullae IS 123(T) (97.4 %), Rhizobium yanglingense SH 22623(T) (97.2 %), Rhizobium gallicum R 602sp(T) (97.1 %), Rhizobium alamii GBV 016(T) (97.0 %), and Rhizobium monogolense USDA 1844(T) (97.0 %). It showed less than 97 % identity with the remaining Rhizobium species. This novel isolate grew optimally at 25-37 °C (optimum, 30 °C) and pH 6-9 (optimum, pH 8.0). It grew in the presence of 0-4 % (w/v) NaCl, tolerating a 4 % (w/v) NaCl. DNA-DNA hybridization experiment shows less than 53 % binding with closely related Rhizobium. Predominant quinone is ubiquinone (Q-10). The major fatty acids were summed feature 8 (composed of C(18:1) ω7c/C(18:1) ω6c), C(19:0) cyclo ω8c, and C(16:0). The G+C molar content is 62.5 mol%. Based on the polyphasic analysis, strain AB21(T) is referred to be a novel species of the genus Rhizobium for which the name Rhizobium halotolerans sp. nov. is proposed. The type strain is AB21(T) (=KEMC 224-056(T) = JCM 17536(T)).

  17. Safety Evaluation of a Novel Strain of Bacteroides fragilis.

    PubMed

    Wang, Ye; Deng, Huimin; Li, Zhengchao; Tan, Yafang; Han, Yanping; Wang, Xiaoyi; Du, Zongmin; Liu, Yangyang; Yang, Ruifu; Bai, Yang; Bi, Yujing; Zhi, Fachao

    2017-01-01

    Commensal non-toxigenic Bacteroides fragilis confers powerful health benefits to the host, and has recently been identified as a promising probiotic candidate. We previously isolated B. fragilis strain ZY-312 and identified it as a novel strain based on 16S rRNA sequencing and morphological analyses. We also determined that ZY-312 displayed desirable probiotic properties, including tolerance to simulated digestive fluid, adherence, and in vitro safety. In this study, we aim to investigate whether ZY-312 meets the safety criteria required for probiotic bacteria through comprehensive and systematic evaluation. Consequently, the fatty acid profile, metabolite production, and biochemical activity of strain ZY-312 were found to closely resemble descriptions of B. fragilis in Bergey's manual. Taxonomic identification of strain ZY-312 based on whole genome sequencing indicated that ZY-312 and ATCC 25285 showed 99.99% similarity. The 33 putative virulence-associated factors identified in ZY-312 mainly encoded structural proteins and proteins with physiological activity, while the lack of bft indicated that ZY-312 was non-toxigenic. In vivo safety was proven in both normal and immune-deficient mice. The 11 identified antibiotic resistance genes were located on the chromosome rather than on a plasmid, ruling out the risk of plasmid-mediated transfer of antibiotic resistance. In vitro, ZY-312 showed resistance to cefepime, kanamycin, and streptomycin. Finally, and notably, ZY-312 exhibited high genetic stability after 100 passages in vitro. This study supplements the foundation work on the safety evaluation of ZY-312, and contributes to the development of the first probiotic representative from the dominant Bacteroidetes phylum.

  18. Safety Evaluation of a Novel Strain of Bacteroides fragilis

    PubMed Central

    Deng, Huimin; Li, Zhengchao; Tan, Yafang; Han, Yanping; Wang, Xiaoyi; Du, Zongmin; Liu, Yangyang; Yang, Ruifu; Bai, Yang; Bi, Yujing; Zhi, Fachao

    2017-01-01

    Commensal non-toxigenic Bacteroides fragilis confers powerful health benefits to the host, and has recently been identified as a promising probiotic candidate. We previously isolated B. fragilis strain ZY-312 and identified it as a novel strain based on 16S rRNA sequencing and morphological analyses. We also determined that ZY-312 displayed desirable probiotic properties, including tolerance to simulated digestive fluid, adherence, and in vitro safety. In this study, we aim to investigate whether ZY-312 meets the safety criteria required for probiotic bacteria through comprehensive and systematic evaluation. Consequently, the fatty acid profile, metabolite production, and biochemical activity of strain ZY-312 were found to closely resemble descriptions of B. fragilis in Bergey’s manual. Taxonomic identification of strain ZY-312 based on whole genome sequencing indicated that ZY-312 and ATCC 25285 showed 99.99% similarity. The 33 putative virulence-associated factors identified in ZY-312 mainly encoded structural proteins and proteins with physiological activity, while the lack of bft indicated that ZY-312 was non-toxigenic. In vivo safety was proven in both normal and immune-deficient mice. The 11 identified antibiotic resistance genes were located on the chromosome rather than on a plasmid, ruling out the risk of plasmid-mediated transfer of antibiotic resistance. In vitro, ZY-312 showed resistance to cefepime, kanamycin, and streptomycin. Finally, and notably, ZY-312 exhibited high genetic stability after 100 passages in vitro. This study supplements the foundation work on the safety evaluation of ZY-312, and contributes to the development of the first probiotic representative from the dominant Bacteroidetes phylum. PMID:28367145

  19. High lipid productivity of an Ankistrodesmus-Rhizobium artificial consortium.

    PubMed

    Do Nascimento, Mauro; Dublan, Maria de los Angeles; Ortiz-Marquez, Juan Cesar Federico; Curatti, Leonardo

    2013-10-01

    Microalgae have great potential as alternative productive platforms for sustainable production of bioenergy, food, feed and other commodities. Process optimization to realize the claimed potential often comprises strains selection and improvement and also developing of more efficient cultivation, harvesting and downstream processing technology. In this work we show that inoculation with the bacterium Rhizobium strain 10II resulted in increments of up to 30% in chlorophyll, biomass and lipids accumulation of the oleaginous microalgae Ankistrodesmus sp. strain SP2-15. Inoculated cultures have reached a high lipid productivity of up to 112 mg L(-1) d(-1) after optimization. The resulting biomass presented significant levels of Ω3 fatty acids including stearidonic acid, suggesting potential as an alternative land-based source of essential fatty acids.

  20. Rhizobium calliandrae sp. nov., Rhizobium mayense sp. nov. and Rhizobium jaguaris sp. nov., rhizobial species nodulating the medicinal legume Calliandra grandiflora.

    PubMed

    Rincón-Rosales, Reiner; Villalobos-Escobedo, José M; Rogel, Marco A; Martinez, Julio; Ormeño-Orrillo, Ernesto; Martínez-Romero, Esperanza

    2013-09-01

    Calliandra grandiflora has been used as a medicinal plant for thousands of years in Mexico. Rhizobial strains were obtained from root nodules of C. grandiflora collected from different geographical regions in Chiapas and characterized by BOX-PCR, amplified rDNA restriction analysis (ARDRA) and 16S rRNA gene sequence analysis. Most isolates corresponded to members of the genus Rhizobium and those not related to species with validly published names were further characterized by recA, atpD, rpoB and nifH gene phylogenies, phenotypic and DNA-DNA hybridization analyses. Three novel related species of the genus Rhizobium within the 'Rhizobium tropici group' share the same symbiovar that may be named sv. calliandrae. The names proposed for the three novel species are Rhizobium calliandrae sp. nov. (type strain, CCGE524(T) =ATCC BAA-2435(T) =CIP 110456(T) =LBP2-1(T)), Rhizobium mayense sp. nov. (type strain, CCGE526(T) =ATCC BAA-2446(T) = CIP 110454(T) =NSJP1-1(T)) and Rhizobium jaguaris sp. nov. (type strain, CCGE525(T) =ATCC BAA-2445(T) =CIP 110453(T) =SJP1-2(T)).

  1. Bacteriophages active against Bacteroides fragilis in sewage-polluted waters.

    PubMed Central

    Tartera, C; Jofre, J

    1987-01-01

    Twelve strains of different Bacteroides species were tested for their efficiency of detection of bacteriophages from sewage. The host range of several isolated phages was investigated. The results indicated that there was a high degree of strain specificity. Then, by using Bacteroides fragilis HSP 40 as the host, which proved to be the most efficient for the detection of phages, feces from humans and several animal species and raw sewage, river water, water from lagoons, seawater, groundwater, and sediments were tested for the presence of bacteriophages that were active against B. fragilis HSP 40. Phages were detected in feces of 10% of the human fecal samples tested and was never detected in feces of the other animal species studied. Moreover, bacteriophages were always recovered from sewage and sewage-polluted samples of waters and sediments, but not from nonpolluted samples. The titers recovered were dependent on the degree of pollution in analyzed waters and sediments. PMID:3662510

  2. Bacteroides pyogenes causing serious human wound infection from animal bites.

    PubMed

    Lau, Jillian S Y; Korman, Tony M; Yeung, Alex; Streitberg, Richard; Francis, Michelle J; Graham, Maryza

    2016-12-01

    Bacteroides pyogenes is part of the normal oral flora of domestic animals. There is one previous report of human infection, with B. pyogenes bacteremia following a cat bite (Madsen 2011). We report seven severe human infections where B. pyogenes was identified by Bruker matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDTI-TOF MS), but not by VITEK MS and was misidentified by VITEK ANC card.

  3. 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.

  4. Putative Porin of Bradyrhizobium sp. (Lupinus) Bacteroids Induced by Glyphosate▿

    PubMed Central

    de María, Nuria; Guevara, Ángeles; Serra, M. Teresa; García-Luque, Isabel; González-Sama, Alfonso; de Lacoba, Mario García; de Felipe, M. Rosario; Fernández-Pascual, Mercedes

    2007-01-01

    Application of glyphosate (N-[phosphonomethyl] glycine) to Bradyrhizobium sp. (Lupinus)-nodulated lupin plants caused modifications in the protein pattern of bacteroids. The most significant change was the presence of a 44-kDa polypeptide in bacteroids from plants treated with the higher doses of glyphosate employed (5 and 10 mM). The polypeptide has been characterized by the amino acid sequencing of its N terminus and the isolation and nucleic acid sequencing of its encoding gene. It is putatively encoded by a single gene, and the protein has been identified as a putative porin. Protein modeling revealed the existence of several domains sharing similarity to different porins, such as a transmembrane beta-barrel. The protein has been designated BLpp, for Bradyrhizobium sp. (Lupinus) putative porin, and would be the first porin described in Bradyrhizobium sp. (Lupinus). In addition, a putative conserved domain of porins has been identified which consists of 87 amino acids, located in the BLpp sequence 30 amino acids downstream of the N-terminal region. In bacteroids, mRNA of the BLpp gene shows a basal constitutive expression that increases under glyphosate treatment, and the expression of the gene is seemingly regulated at the transcriptional level. By contrast, in free-living bacteria glyphosate treatment leads to an inhibition of BLpp mRNA accumulation, indicating a different effect of glyphosate on BLpp gene expression in bacteroids and free-living bacteria. The possible role of BLpp in a metabolite interchange between Bradyrhizobium and lupin is discussed. PMID:17557843

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

    PubMed Central

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

    1995-01-01

    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

  6. 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…

  7. 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.

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

    PubMed

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

    2014-11-01

    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 impacted its development by decreasing the number of the first- and the second-order lateral roots, stem length, leaf surface area, and transpiration. The effect of nZnO dissolution on phytotoxicity was also examined. Results showed that Zn(2+) had negative impact on plant development. Exposure of R. leguminosarum bv. viciae 3841 to nZnO brought about morphological changes by rendering the microbial cells toward round shape and damaging the bacterial surface. Furthermore, the presence of nZnO in the rhizosphere affected root nodulation, delayed the onset of nitrogen fixation, and caused early senescence of nodules. Attachment of nanoparticles on the root surface and dissolution of Zn(2+) are important factors affecting the phytotocity of nZnO. Hence, the presence of nZnO in the environment is potentially hazardous to the Rhizobium-legume symbiosis system.

  9. Rhizobium yantingense sp. nov., a mineral-weathering bacterium.

    PubMed

    Chen, Wei; Sheng, Xia-Fang; He, Lin-Yan; Huang, Zhi

    2015-02-01

    A Gram-stain-negative, rod-shaped bacterial strain, H66(T), was isolated from the surfaces of weathered rock (purple siltstone) found in Yanting, Sichuan Province, PR China. Cells of strain H66(T) were motile with peritrichous flagella. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain H66(T) belongs to the genus Rhizobium. It is closely related to Rhizobium huautlense SO2(T) (98.1 %), Rhizobium alkalisoli CCBAU 01393(T) (98.0 %) and Rhizobium cellulosilyticum ALA10B2(T) (98.0 %). Analysis of the housekeeping genes, recA, glnII and atpD, showed low levels of sequence similarity (<92.0 %) between strain H66(T) and other recognized species of the genus Rhizobium. The predominant components of the cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The G+C content of strain H66(T) was 60.3 mol%. Strain H66(T) is suggested to be a novel species of the genus Rhizobium based on the low levels of DNA-DNA relatedness (ranging from 14.3 % to 40.0 %) with type strains of species of the genus Rhizobium and on its unique phenotypic characteristics. The namehttp://dx.doi.org/10.1601/nm.1279Rhizobium yantingense sp. nov. is proposed for this novel species. The type strain is H66(T) ( = CCTCC AB 2014007(T) = LMG 28229(T)).

  10. Rhizobium-legume symbiosis shares an exocytotic pathway required for arbuscule formation.

    PubMed

    Ivanov, Sergey; Fedorova, Elena E; Limpens, Erik; De Mita, Stephane; Genre, Andrea; Bonfante, Paola; Bisseling, Ton

    2012-05-22

    Endosymbiotic interactions are characterized by the formation of specialized membrane compartments, by the host in which the microbes are hosted, in an intracellular manner. Two well-studied examples, which are of major agricultural and ecological importance, are the widespread arbuscular mycorrhizal symbiosis and the Rhizobium-legume symbiosis. In both symbioses, the specialized host membrane that surrounds the microbes forms a symbiotic interface, which facilitates the exchange of, for example, nutrients in a controlled manner and, therefore, forms the heart of endosymbiosis. Despite their key importance, the molecular and cellular mechanisms underlying the formation of these membrane interfaces are largely unknown. Recent studies strongly suggest that the Rhizobium-legume symbiosis coopted a signaling pathway, including receptor, from the more ancient arbuscular mycorrhizal symbiosis to form a symbiotic interface. Here, we show that two highly homologous exocytotic vesicle-associated membrane proteins (VAMPs) are required for formation of the symbiotic membrane interface in both interactions. Silencing of these Medicago VAMP72 genes has a minor effect on nonsymbiotic plant development and nodule formation. However, it blocks symbiosome as well as arbuscule formation, whereas root colonization by the microbes is not affected. Identification of these VAMP72s as common symbiotic regulators in exocytotic vesicle trafficking suggests that the ancient exocytotic pathway forming the periarbuscular membrane compartment has also been coopted in the Rhizobium-legume symbiosis.

  11. Widespread fitness alignment in the legume-rhizobium symbiosis.

    PubMed

    Friesen, Maren L

    2012-06-01

    Although 'cheaters' potentially destabilize the legume-rhizobium mutualism, we lack a comprehensive review of host-symbiont fitness correlations. Studies measuring rhizobium relative or absolute fitness and host benefit are surveyed. Mutant studies are tallied for evidence of pleiotropy; studies of natural strains are analyzed with meta-analysis. Of 80 rhizobium mutations, 19 decrease both partners' fitness, four increase both, two increase host fitness but decrease symbiont fitness and none increase symbiont fitness at the host's expense. The pooled correlation between rhizobium nodulation competitiveness and plant aboveground biomass is 0.65 across five experiments that compete natural strains against a reference, whereas, across 14 experiments that compete rhizobia against soil populations or each other, the pooled correlation is 0.24. Pooled correlations between aboveground biomass and nodule number and nodule biomass are 0.76 and 0.83. Positive correlations between legume and rhizobium fitness imply that most ineffective rhizobia are 'defective' rather than 'defectors'; this extends to natural variants, with only one significant fitness conflict. Most studies involve non-coevolved associations, indicating that fitness alignment is the default state. Rhizobium mutations that increase both host and symbiont fitness suggest that some plants maladaptively restrict symbiosis with novel strains.

  12. Optimization of dairy sludge for growth of Rhizobium cells.

    PubMed

    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.

  13. Reiterated DNA sequences in Rhizobium and Agrobacterium spp.

    PubMed Central

    Flores, M; González, V; Brom, S; Martínez, E; Piñero, D; Romero, D; Dávila, G; Palacios, R

    1987-01-01

    Repeated DNA sequences are a general characteristic of eucaryotic genomes. Although several examples of DNA reiteration have been found in procaryotic organisms, only in the case of the archaebacteria Halobacterium halobium and Halobacterium volcanii [C. Sapienza and W. F. Doolittle, Nature (London) 295:384-389, 1982], has DNA reiteration been reported as a common genomic feature. The genomes of two Rhizobium phaseoli strains, one Rhizobium meliloti strain, and one Agrobacterium tumefaciens strain were analyzed for the presence of repetitive DNA. Rhizobium and Agrobacterium spp. are closely related soil bacteria that interact with plants and that belong to the taxonomical family Rhizobiaceae. Rhizobium species establish a nitrogen-fixing symbiosis in the roots of legumes, whereas Agrobacterium species is a pathogen in different plants. The four strains revealed a large number of repeated DNA sequences. The family size was usually small, from 2 to 5 elements, but some presented more than 10 elements. Rhizobium and Agrobacterium spp. contain large plasmids in addition to the chromosomes. Analysis of the two Rhizobium strains indicated that DNA reiteration is not confined to the chromosome or to some plasmids but is a property of the whole genome. Images PMID:3450286

  14. 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

  15. Rhizobium herbae sp. nov. and Rhizobium giardinii-related bacteria, minor microsymbionts of various wild legumes in China.

    PubMed

    Ren, Da Wei; Wang, En Tao; Chen, Wen Feng; Sui, Xin Hua; Zhang, Xiao Xia; Liu, Hong Can; Chen, Wen Xin

    2011-08-01

    Seven Rhizobium strains associated with various legume species grown in different geographical regions of China were defined into four genomic groups related to Rhizobium giardinii, based upon ribosomal intergenic spacer RFLP, phylogenies of 16S rRNA and housekeeping (atpD, recA and glnII) genes, and DNA relatedness. Three strains in group I were classified as R. giardinii, as they showed high gene sequence similarities (>97 %) and DNA relatedness (64.3-67.5 %) to R. giardinii H152(T). Groups II, III and IV differed from all defined Rhizobium species based upon the consensus of all analyses. As group II contained two strains that originated from two distinct populations, we propose this group as a novel species, Rhizobium herbae sp. nov., with strain CCBAU 83011(T) ( = LMG 25718(T) = HAMBI 3117(T)) as the type strain.

  16. 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

  17. Bacteriophages infecting Bacteroides as a marker for microbial source tracking.

    PubMed

    Jofre, Joan; Blanch, Anicet R; Lucena, Francisco; Muniesa, Maite

    2014-05-15

    Bacteriophages infecting certain strains of Bacteroides are amid the numerous procedures proposed for tracking the source of faecal pollution. These bacteriophages fulfil reasonably well most of the requirements identified as appropriate for a suitable marker of faecal sources. Thus, different host strains are available that detect bacteriophages preferably in water contaminated with faecal wastes corresponding to different animal species. For phages found preferably in human faecal wastes, which are the ones that have been more extensively studied, the amounts of phages found in waters contaminated with human fecal samples is reasonably high; these amounts are invariable through the time; their resistance to natural and anthropogenic stressors is comparable to that of other relatively resistant indicator of faecal pollution such us coliphages; the abundance ratios of somatic coliphages and bacteriophages infecting Bacteroides thetaiotaomicron GA17 are unvarying in recent and aged contamination; and standardised detection methods exist. These methods are easy, cost effective and provide data susceptible of numerical analysis. In contrast, there are some uncertainties regarding their geographical stability, and consequently suitable hosts need to be isolated for different geographical areas. However, a feasible method has been described to isolate suitable hosts in a given geographical area. In summary, phages infecting Bacteroides are a marker of faecal sources that in our opinion merits being included in the "toolbox" for microbial source tracking. However, further research is still needed in order to make clear some uncertainties regarding some of their characteristics and behaviour, to compare their suitability to the one of emerging methods such us targeting Bacteroidetes by qPCR assays; or settling molecular methods for their determination.

  18. 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.

  19. Serogrouping of Bacteroides fragilis subsp. fragilis by the agglutination test.

    PubMed Central

    Lambe, D W; Moroz, D A

    1976-01-01

    The agglutination technique was used to establish a serological classification scheme for 98 strains of Bacteroides fragilis subsp. fragilis isolated from clinical specimens and normal human feces. Absorbed antisera were prepared to seven strains of B. fragilis subsp. fragilis. These seven absorbed antisera were species as well as subspecies specific and provided the basis of the serological classification scheme. This scheme was composed of 21 serogroups; seven of these serogroups contained only one group component. There was a total of 45 serological patterns. This serological scheme may be used for the serological classification of strains of B. fragilis subsp. fragilis and to study the epidemiology of this organism. PMID:950378

  20. Bacteroids Are Stable during Dark-Induced Senescence of Soybean Root Nodules 12

    PubMed Central

    Sarath, Gautam; Pfeiffer, Nancy E.; Sodhi, C. S.; Wagner, Fred W.

    1986-01-01

    Physiological and biochemical markers of metabolic competence were assayed in bacteroids isolated from root nodules of control, dark-stressed, and recovered plants of Glycine max Merr. cv `Woodworth.' Nitrogenase-dependent acetylene reduction by the whole plant decreased to 8% of control rates after 4 days of dark stress and could not be detected in plants dark stressed for 8 days. However, in bacteroids isolated anaerobically, almost 50% of initial acetylene reduction activity remained after 4 days of dark stress but was totally lost after 8 days of dark stress. Bacteroid acetylene reduction activity recovered faster than whole plant acetylene reduction activity when plants were dark stressed for 8 days and returned to a normal light regimen. Significant changes were not measured in bacteroid respiration, protein content, sodium dodecyl sulfate-polyacrylamide gel electrophoresis protein profiles, or in bacteroid proteolytic activity throughout the experiment. Immunoblots of bacteroid extracts revealed the presence of nitrogenase component II in control, 4-day dark-stressed, and 8-day dark-stressed plants that were allowed to recover under a normal light regimen, but not in 8-day dark-stressed plants. Our data indicate that dark stress does not greatly affect bacteroid metabolism or induce bacteroid senescence. Images Fig. 2 Fig. 3 PMID:16665033

  1. 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).

  2. Genetic Structure of Rhizobium etli biovar phaseoli Associated with Wild and Cultivated Bean Plants (Phaseolus vulgaris and Phaseolus coccineus) in Morelos, Mexico

    PubMed Central

    Souza, Valeria; Eguiarte, Luis; Avila, German; Cappello, Renato; Gallardo, Claudia; Montoya, Javier; Piñero, Daniel

    1994-01-01

    The genetic structure of Rhizobium etli biovar phaseoli was determined for five populations in three different locations in the state of Morelos, Mexico, by using starch gel electrophoresis for five to nine polymorphic loci. Two populations were sampled during two different years from nodules of cultivated and wild common bean plants (Phaseolus vulgaris). The three other populations were associated with wild runner beans (P. coccineus) and sampled during 1988. The Rhizobium populations differ genetically both among sites and among populations within the same site in different years, as shown by differences in allelic frequencies, genetic differentiation analysis, and differences in electrotypes. The total genetic diversity for the five populations during 1988 was H = 0.487; there were also high levels of genetic variation within each population. We found the highest linkage disequilibrium in a global analysis for all the populations. At a local scale, we also found significant linkage disequilibrium in two populations, although the distribution of the D′ suggest some recombination at a local scale. The other three rhizobium populations exhibit low linkage disequilibrium. A cluster analysis (UPGMA) of pairwise genetic distances showed that bacteria isolated from most wild Phaseolus spp. are grouped by population, whereas those obtained from cultivated P. vulgaris are very heterogeneous. The analysis of the genetic structure of Rhizobium strains may allow the identification of strains that are naturally well adapted to a wide range of different environments, which may be useful for agricultural purposes or as a starting point for developing improved Rhizobium strains. PMID:16349234

  3. Serological identification of oral Bacteroides spp. by enzyme-linked immunosorbent assay.

    PubMed Central

    Ebersole, J L; Frey, D E; Taubman, M A; Smith, D J; Socransky, S S; Tanner, A C

    1984-01-01

    A rapid method for identifying black-pigmented oral Bacteroides spp. is described. Species-specific rabbit antisera to Bacteroides gingivalis, B. intermedius, and B. melaninogenicus were used in an enzyme-linked immunosorbent assay to identify clinical isolates of black-pigmented Bacteroides spp. from humans. The results showed excellent agreement with biochemical identification of B. gingivalis and B. intermedius. Only 36% of the B. melaninogenicus isolates were identified with the enzyme-linked immunosorbent assay, suggesting that this group of black-pigmented Bacteroides spp. is made up of more than one serotype. The serological enzyme-linked immunosorbent assay should enable rapid identification of black-pigmented Bacteroides spp. isolated from sites of oral diseases and may also be used to identify the presence of these organisms in complex bacterial mixtures from oral sites. PMID:6736225

  4. Analysis of synonymous codon usage patterns in the genus Rhizobium.

    PubMed

    Wang, Xinxin; Wu, Liang; Zhou, Ping; Zhu, Shengfeng; An, Wei; Chen, Yu; Zhao, Lin

    2013-11-01

    The codon usage patterns of rhizobia have received increasing attention. However, little information is available regarding the conserved features of the codon usage patterns in a typical rhizobial genus. The codon usage patterns of six completely sequenced strains belonging to the genus Rhizobium were analysed as model rhizobia in the present study. The relative neutrality plot showed that selection pressure played a role in codon usage in the genus Rhizobium. Spearman's rank correlation analysis combined with correspondence analysis (COA) showed that the codon adaptation index and the effective number of codons (ENC) had strong correlation with the first axis of the COA, which indicated the important role of gene expression level and the ENC in the codon usage patterns in this genus. The relative synonymous codon usage of Cys codons had the strongest correlation with the second axis of the COA. Accordingly, the usage of Cys codons was another important factor that shaped the codon usage patterns in Rhizobium genomes and was a conserved feature of the genus. Moreover, the comparison of codon usage between highly and lowly expressed genes showed that 20 unique preferred codons were shared among Rhizobium genomes, revealing another conserved feature of the genus. This is the first report of the codon usage patterns in the genus Rhizobium.

  5. Characterisation of SalRAB a salicylic acid inducible positively regulated efflux system of Rhizobium leguminosarum bv viciae 3841.

    PubMed

    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.

  6. Light regulates attachment, exopolysaccharide production, and nodulation in Rhizobium leguminosarum through a LOV-histidine kinase photoreceptor.

    PubMed

    Bonomi, Hernán R; Posadas, Diana M; Paris, Gastón; Carrica, Mariela del Carmen; Frederickson, Marcus; Pietrasanta, Lía Isabel; Bogomolni, Roberto A; Zorreguieta, Angeles; Goldbaum, Fernando A

    2012-07-24

    Rhizobium leguminosarum is a soil bacterium that infects root hairs and induces the formation of nitrogen-fixing nodules on leguminous plants. Light, oxygen, and voltage (LOV)-domain proteins are blue-light receptors found in higher plants and many algae, fungi, and bacteria. The genome of R. leguminosarum bv. viciae 3841, a pea-nodulating endosymbiont, encodes a sensor histidine kinase containing a LOV domain at the N-terminal end (R-LOV-HK). R-LOV-HK has a typical LOV domain absorption spectrum with broad bands in the blue and UV-A regions and shows a truncated photocycle. Here we show that the R-LOV-HK protein regulates attachment to an abiotic surface and production of flagellar proteins and exopolysaccharide in response to light. Also, illumination of bacterial cultures before inoculation of pea roots increases the number of nodules per plant and the number of intranodular bacteroids. The effects of light on nodulation are dependent on a functional lov gene. The results presented in this work suggest that light, sensed by R-LOV-HK, is an important environmental factor that controls adaptive responses and the symbiotic efficiency of R. leguminosarum.

  7. Conservation of Plasmid-Encoded Traits among Bean-Nodulating Rhizobium Species

    PubMed Central

    Brom, Susana; Girard, Lourdes; García-de los Santos, Alejandro; Sanjuan-Pinilla, Julio M.; Olivares, José; Sanjuan, Juan

    2002-01-01

    Rhizobium etli type strain CFN42 contains six plasmids. We analyzed the distribution of genetic markers from some of these plasmids in bean-nodulating strains belonging to different species (Rhizobium etli, Rhizobium gallicum, Rhizobium giardinii, Rhizobium leguminosarum, and Sinorhizobium fredii). Our results indicate that independent of geographic origin, R. etli strains usually share not only the pSym plasmid but also other plasmids containing symbiosis-related genes, with a similar organization. In contrast, strains belonging to other bean-nodulating species seem to have acquired only the pSym plasmid from R. etli. PMID:11976134

  8. A Rhizobium meliloti symbiotic regulatory gene.

    PubMed

    Szeto, W W; Zimmerman, J L; Sundaresan, V; Ausubel, F M

    1984-04-01

    We have characterized a Rhizobium meliloti regulatory gene required for the expression of two closely linked symbiotic operons, the nitrogenase operon (nifHDK genes) and the "P2" operon. This regulatory gene maps to a 1.8 kb region located 5.5 kb upstream of the nifHDK operon. The regulatory gene is required for the accumulation of nifHDK and P2 mRNA and for the derepression of an R. meliloti nifH-lacZ fusion plasmid during symbiotic growth. The nifH and P2 promoters can be activated in free-living cultures of R. meliloti containing plasmids that produce the Escherichia coli ntrC(glnG) or the Klebsiella pneumoniae nifA regulatory gene products constitutively. The R. meliloti regulatory gene hybridizes to E. coli ntrC(glnG) and, to a lesser extent, to K. pneumoniae nifA DNA. Our results suggest that the R. meliloti regulatory gene acts as a positive transcriptional activator and that it is related to the K. pneumoniae nif regulatory genes.

  9. Variations in exopolysaccharide production by Rhizobium tropici.

    PubMed

    Staudt, Ann K; Wolfe, Lawrence G; Shrout, Joshua D

    2012-03-01

    Rhizobium tropici, a legume-symbiont soil bacterium, is known for its copious production of exopolysaccharide (EPS). Many aspects of this organism's growth and EPS production, however, remain uncharacterized, including the influence of environment and culturing conditions upon EPS. Here, we demonstrate that R. tropici EPS chemical composition and yield differ when grown with different substrates in a defined minimal medium in batch culture. Exopolysaccharide was quantified from R. tropici grown using arabinose, glucose, sucrose, mannitol, fructose, or glutamate as a sole carbon source. All tested substrates produced plenteous amounts of exopolysaccharide material. Variations in pH and carbon-to-nitrogen (C/N) ratio also resulted in assorted cell growth and exopolysaccharide production differences. We found that optimizing the C/N ratio has a greater impact upon R. tropici EPS production than upon R. tropici growth. A maximum EPS yield of 4.08 g/L was realized under optimized conditions, which is large even in comparison with other known rhizobia. We provide evidence that the chemical composition of R. tropici EPS can vary with changes to the growth environment. The composition of glucose-grown EPS contained rhamnose-linked residues that were not present in arabinose-grown EPS.

  10. 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.

  11. Metronidazole and spiramycin therapy of mixed Bacteroides spp. and Neisseria gonorrhoeae infection in mice.

    PubMed

    Brook, I

    1989-01-01

    The in vitro and in vivo activity of metronidazole and spiramycin, used singly or in combination, was tested in the eradication of infection caused by Bacteroides spp. and Neisseria gonorrhoeae alone or in combination. The in vitro tests consisted of determinations of the minimal inhibitory concentrations (MIC), carried out with or without the addition of a constant amount of the other antimicrobials. The MIC of both Bacteroides bivius and Bacteroides fragilis for metronidazole were significantly reduced by the addition of spiramycin (from 0.5 to 0.125 micrograms/ml). The in vivo tests were carried out in mice and consisted of measurements of the effects of the antimicrobial agents on the bacterial contents of abscesses induced by subcutaneous injection of bacterial suspension. Synergism between metronidazole and spiramycin was noted against Bacteroides spp. in abscesses caused by either Bacteroides spp. alone, or in combination with N. gonorrhoeae. Furthermore, an additional reduction in the number of N gonorrhoeae was noted in mixed infection with Bacteroides that was treated with metronidazole alone. This study demonstrates the in vitro and in vivo efficacy of the combination of metronidazole and spiramycin in the treatment of infections caused by either Bacteroides spp. alone or in combination with N. gonorrhoeae.

  12. Peribacteroid space acidification: a marker of mature bacteroid functioning in Medicago truncatula nodules.

    PubMed

    Pierre, Olivier; Engler, Gilbert; Hopkins, Julie; Brau, Frédéric; Boncompagni, Eric; Hérouart, Didier

    2013-11-01

    Legumes form a symbiotic interaction with Rhizobiaceae bacteria, which differentiate into nitrogen-fixing bacteroids within nodules. Here, we investigated in vivo the pH of the peribacteroid space (PBS) surrounding the bacteroid and pH variation throughout symbiosis. In vivo confocal microscopy investigations, using acidotropic probes, demonstrated the acidic state of the PBS. In planta analysis of nodule senescence induced by distinct biological processes drastically increased PBS pH in the N2 -fixing zone (zone III). Therefore, the PBS acidification observed in mature bacteroids can be considered as a marker of bacteroid N2 fixation. Using a pH-sensitive ratiometric probe, PBS pH was measured in vivo during the whole symbiotic process. We showed a progressive acidification of the PBS from the bacteroid release up to the onset of N2 fixation. Genetic and pharmacological approaches were conducted and led to disruption of the PBS acidification. Altogether, our findings shed light on the role of PBS pH of mature bacteroids in nodule functioning, providing new tools to monitor in vivo bacteroid physiology.

  13. [LEGUME-RHIZOBIUM SYMBIOSIS PROTEOMICS: ACHIEVEMENTS AND PERSPECTIVES].

    PubMed

    Kondratiuk, Iu Iu; Mamenko, P M; Kots, S Ya

    2015-01-01

    The present review contains results of proteomic researches of legume-rhizobium symbiosis. The technical difficulties associated with the methods of obtaining protein extracts from symbiotic structures and ways of overcoming them were discussed. The changes of protein synthesis under formation and functioning of symbiotic structures were shown. Special attention has been given to the importance of proteomic studies of plant-microbe structures in the formation of adaptation strategies under adverse environmental conditions. The technical and conceptual perspectives of legume-rhizobium symbiosis proteomics were shown.

  14. Rhizobium-legume symbioses: the crucial role of plant immunity.

    PubMed

    Gourion, Benjamin; Berrabah, Fathi; Ratet, Pascal; Stacey, Gary

    2015-03-01

    New research results have significantly revised our understanding of the rhizobium-legume infection process. For example, Nod factors (NFs), previously thought to be absolutely essential for this symbiosis, were shown to be dispensable under particular conditions. Similarly, an NF receptor, previously considered to be solely involved in symbiosis, was shown to function during plant pathogen infections. Indeed, there is a growing realization that plant innate immunity is a crucial component in the establishment and maintenance of symbiosis. We review here the factors involved in the suppression of plant immunity during rhizobium-legume symbiosis, and we attempt to place this information into context with the most recent and sometimes surprising research results.

  15. Heme compounds as iron sources for nonpathogenic Rhizobium bacteria.

    PubMed Central

    Noya, F; Arias, A; Fabiano, E

    1997-01-01

    Many animal-pathogenic bacteria can use heme compounds as iron sources. Like these microorganisms, rhizobium strains interact with host organisms where heme compounds are available. Results presented in this paper indicate that the use of hemoglobin as an iron source is not restricted to animal-pathogenic microorganisms. We also demonstrate that heme, hemoglobin, and leghemoglobin can act as iron sources under iron-depleted conditions for Rhizobium meliloti 242. Analysis of iron acquisition mutant strains indicates that siderophore-, heme-, hemoglobin-, and leghemoglobin-mediated iron transport systems expressed by R. meliloti 242 share at least one component. PMID:9139934

  16. Antibacterial action of natural honey on anaerobic bacteroides.

    PubMed

    Elbagoury, E F; Rasmy, S

    1993-01-01

    Two samples of natural Honey were tested for their antibacterial effect on Bacteroides, mainly the pathogenic black pigmented B. melaninogenicus isolated from ten cases of dental infections (dental abscesses and chronic osteomyelitis). These organisms were subjected to the effect of natural and diluted honey (50%), in broth and solid cultures. The results were compared with those of the same organisms incubated with saturated glucose solution, which showed less inhibition, indicating that the inhibitory effect of honey was not due to its high sugar content nor to its acidic PH, when using Schaedler's broth adjusted to the same PH as control. The local therapeutic value of natural honey was illustrated with an attempt to correlate between the microbial findings and the clinical implications.

  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. 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.

  19. 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

  20. 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.

  1. Rhizobium (Agrobacterium) radiobacter identified as a cause of chronic endophthalmitis subsequent to cataract extraction.

    PubMed

    Namdari, Hassan; Hamzavi, Sirus; Peairs, Randall R

    2003-08-01

    Herein, we report a case of chronic endophthalmitis caused by a ceftazidime-resistant Rhizobium radiobacter strain in a 62-year-old male. The patient underwent an uneventful cataract extraction of the right eye a week prior to the appearance of symptoms (pain, redness, and blurring vision) which developed following a golf outing. Upon admission the patient received an emergency vitrectomy. The patient remained symptomatic, and R. radiobacter was isolated repeatedly from vitreous fluid cultures over a 5-month period. Ultimately, the infection responded to intravitreal gentamicin, oral ciprofloxacin, and removal of the lens implant.

  2. Specificity of immunoglobulin M antibodies in normal human serum that participate in opsonophagocytosis and intracellular killing of Bacteroides fragilis and Bacteroides thetaiotaomicron by by human polymorphonuclear leukocytes.

    PubMed Central

    Bjornson, A B; Bjornson, H S; Kitko, B P

    1980-01-01

    Studies were performed to determine the specificity of immunoglobulin M (IgM) antibodies in normal human serum that participate in opsonophagocytosis and intracellular killing of Bacteroides fragilis 1365 and Bacteroides thetaiotaomicron 1343 by human polymorphonuclear leukocytes. Purified normal human IgM was adsorbed with washed heat-killed cells of the homologous strains and heterologous strains of B. fragilis, B. thetaiotaomicron, Bacteroides vulgatus, Bacteroides distasonis, and Bacteroides asaccharolyticus and with erythrocytes coated with outer membrane complex prepared from the homologous strains. Hypogammaglobulinemic serum was supplemented with the adsorbed IgM preparations, and the ability of the supplemented sera to support opsonophagocytosis and killing of B. fragilis 1365 and B. thetaiotaomicron 1343 by human polymorphonuclear leukocytes was measured in vitro under anaerobic conditions. Normal IgM adsorbed with heat-killed cells of B. fragilis 1365 and B. thetaiotaomicron 1343 or with erythrocytes coated with outer membrane complex prepared from these strains failed to restore the ability of hypogammaglobulinemic serum to support opsonophagocytosis and intracellular killing of the homologous strain. In contrast, adsorption of normal IgM with heat-killed cells of the heterologous strains did not alter its opsonophagocytosis-promoting activity for either test strain. These results indicated that the IgM antibodies in normal human serum that participate in opsonophagocytosis and intracellular killing of B. fragilis 1365 and B. thetaiotaomicron 1343 are directed against strain-specific antigenic determinants contained in the outer membrane complex. Images Fig. 5 Fig. 6 PMID:6160104

  3. Distinct Mineral Weathering Behaviors of the Novel Mineral-Weathering Strains Rhizobium yantingense H66 and Rhizobium etli CFN42

    PubMed Central

    Chen, Wei; Luo, Long; He, Lin-Yan; Wang, Qi

    2016-01-01

    ABSTRACT Bacteria play important roles in mineral weathering, soil formation, and element cycling. However, little is known about the interaction between silicate minerals and rhizobia. In this study, Rhizobium yantingense H66 (a novel mineral-weathering rhizobium) and Rhizobium etli CFN42 were compared with respect to potash feldspar weathering, mineral surface adsorption, and metabolic activity during the mineral weathering process. Strain H66 showed significantly higher Si, Al, and K mobilization from the mineral and higher ratios of cell numbers on the mineral surface to total cell numbers than strain CFN42. Although the two strains produced gluconic acid, strain H66 also produced acetic, malic, and succinic acids during mineral weathering in low- and high-glucose media. Notably, higher Si, Al, and K releases, higher ratios of cell numbers on the mineral surface to total cell numbers, and a higher production of organic acids by strain H66 were observed in the low-glucose medium than in the high-glucose medium. Scanning electron microscope analyses of the mineral surfaces and redundancy analysis showed stronger positive correlations between the mineral surface cell adsorption and mineral weathering, indicated by the dissolved Al and K concentrations. The results showed that the two rhizobia behaved differently with respect to mineral weathering. The results suggested that Rhizobium yantingense H66 promoted potash feldspar weathering through increased adsorption of cells to the mineral surface and through differences in glucose metabolism at low and high nutrient concentrations, especially at low nutrient concentrations. IMPORTANCE This study reported the potash feldspar weathering, the cell adsorption capacity of the mineral surfaces, and the metabolic differences between the novel mineral-weathering Rhizobium yantingense H66 and Rhizobium etli CFN42 under different nutritional conditions. The results showed that Rhizobium yantingense H66 had a greater ability

  4. 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...

  5. Rhizobium laguerreae sp. nov. nodulates Vicia faba on several continents.

    PubMed

    Saïdi, Sabrine; Ramírez-Bahena, Martha-Helena; Santillana, Nery; Zúñiga, Doris; Álvarez-Martínez, Estela; Peix, Alvaro; Mhamdi, Ridha; Velázquez, Encarna

    2014-01-01

    Several fast-growing strains nodulating Vicia faba in Peru, Spain and Tunisia formed a cluster related to Rhizobium leguminosarum. The 16S rRNA gene sequences were identical to that of R. leguminosarum USDA 2370(T), whereas rpoB, recA and atpD gene sequences were phylogenetically distant, with sequence similarities of less than 96 %, 97 % and 94 %, respectively. DNA-DNA hybridization analysis showed a mean relatedness value of 43 % between strain FB206(T) and R. leguminosarum USDA 2370(T). Phenotypic characteristics of the novel strains also differed from those of the closest related species of the genus Rhizobium. Therefore, based on genotypic and phenotypic data obtained in this study, we propose to classify this group of strains nodulating Vicia faba as a novel species of the genus Rhizobium named Rhizobium laguerreae sp. nov. The type strain is FB206(T) ( = LMG 27434(T) = CECT 8280(T)).

  6. 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...

  7. 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.

  8. 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.

  9. Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC139T)

    PubMed Central

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

    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. PMID:21677860

  10. Infection of soybean and pea nodules by Rhizobium spp. purine auxotrophs in the presence of 5-aminoimidazole-4-carboxamide riboside.

    PubMed Central

    Newman, J D; Diebold, R J; Schultz, B W; Noel, K D

    1994-01-01

    Purine auxotrophs of various Rhizobium species are symbiotically defective, usually unable to initiate or complete the infection process. Earlier studies demonstrated that, in the Rhizobium etli-bean symbiosis, infection by purine auxotrophs is partially restored by supplementation of the plant medium with 5-amino-imidazole-4-carboxamide (AICA) riboside, the unphosphorylated form of the purine biosynthetic intermediate AICAR. The addition of purine to the root environment does not have this effect. In this study, purine auxotrophs of Rhizobium fredii HH303 and Rhizobium leguminosarum 128C56 (bv. viciae) were examined. Nutritional and genetic characterization indicated that each mutant was blocked in purine biosynthesis prior to the production of AICAR. R. fredii HH303 and R. leguminosarum 128C56 appeared to be deficient in AICA riboside transport and/or conversion into AICAR, and the auxotrophs derived from them grew very poorly with AICA riboside as a purine source. All of the auxotrophs elicited poorly developed, uninfected nodules on their appropriate hosts. On peas, addition of AICA riboside or purine to the root environment led to enhanced nodulation; however, infection threads were observed only in the presence of AICA riboside. On soybeans, only AICA riboside was effective in enhancing nodulation and promoting infection. Although AICA riboside supplementation of the auxotrophs led to infection thread development on both hosts, the numbers of bacteria recovered from the nodules were still 2 or more orders of magnitude lower than in fully developed nodules populated by wild-type bacteria. The ability to AICA riboside to promote infection by purine auxotrophs, despite serving as a very poor purine source for these strains, supports the hypothesis that AICAR plays a role in infection other than merely promoting bacterial growth. Images PMID:8195084

  11. 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)).

  12. Rhizobium lemnae sp. nov., a bacterial endophyte of Lemna aequinoctialis.

    PubMed

    Kittiwongwattana, Chokchai; Thawai, Chitti

    2014-07-01

    Bacterial strain L6-16(T) was isolated from Lemna aequinoctialis. Cells were Gram-stain-negative, rod-shaped and motile with monopolar flagella. The phylogenetic analysis of its nearly complete 16S rRNA gene sequence revealed that strain L6-16(T) was a member of the genus Rhizobium. Its closest relative was Rhizobium tarimense PL-41(T) with a 16S rRNA gene sequence similarity value of 98.3%. Sequence similarity analysis of the housekeeping recA and atpD genes showed low levels of sequence similarity (<93.9%) between strain L6-16(T) and other species of the genus Rhizobium. Strain L6-16(T) was able to grow between pH 5 and 11 (optimum 7.0) and at temperatures ranging from 20 to 41 °C (optimum 30 °C). It tolerated NaCl up to 1 % (w/v) (optimum 0.5%). C18 : 1ω7c and/or C18 :  1ω6c (summed feature 8; 79.5%) were found as predominant cellular fatty acids. The DNA G+C content of strain L6-16(T) was 58.1 mol% (Tm). Based on low levels of DNA-DNA relatedness, strain L6-16(T) was distinct from members of phylogenetically related species including R. tarimense PL-41(T) (38.3 ± 0.8%), Rhizobium rosettiformans W3(T) (6.9 ± 0.4%) and Rhizobium pseudoryzae J3-A127(T) (12.3 ± 0.6 %). Strain L6-16(T) was unable to nodulate the roots of Phaseolus vulgaris, and nodC and nifH genes were not detected. The results obtained from phylogenetic analyses, phenotypic characterization and DNA-DNA hybridization indicated that strain L6-16(T) represents a novel species of the genus Rhizobium, for which the name Rhizobium lemnae sp. nov. is proposed. The type strain is L6-16(T) ( = NBRC 109339(T) = BCC 55143(T)).

  13. 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.

  14. Rhizobium rhizoryzae sp. nov., isolated from rice roots.

    PubMed

    Zhang, Xiao-Xia; Tang, Xue; Sheirdil, Rizwan Ali; Sun, Lei; Ma, Xiao-Tong

    2014-04-01

    Two strains (J3-AN59(T) and J3-N84) of Gram-stain-negative, aerobic and rod-shaped bacteria were isolated from the roots of fresh rice plants. The 16S rRNA gene sequence similarity results showed that the similarity between strains J3-AN59(T) and J3-N84 was 100 %. Both strains were phylogenetically related to members of the genus Rhizobium, and they were most closely related to Rhizobium tarimense ACCC 06128(T) (97.43 %). Similarities in the sequences of housekeeping genes between strains J3-AN59(T) and J3-N84 and those of recognized species of the genus Rhizobium were less than 90 %. The polar lipid profiles of both strains were predominantly composed of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unknown aminophospholipid. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The DNA G+C contents of J3-AN59(T) and J3-N84 were 55.7 and 57.1 mol%, respectively. The DNA-DNA relatedness value between J3-AN59(T) and J3-N84 was 89 %, and strain J3-AN59(T) showed 9 % DNA-DNA relatedness to R. tarimense ACCC 06128(T), the most closely related strain. Based on this evidence, we found that J3-AN59(T) and J3-N84 represent a novel species in the genus Rhizobium and we propose the name Rhizobium rhizoryzae sp. nov. The type strain is J3-AN59(T) ( = ACCC 05916(T) = KCTC 23652(T)).

  15. Rhizobium alvei sp. nov., isolated from a freshwater river.

    PubMed

    Sheu, Shih-Yi; Huang, Hsing-Wei; Young, Chiu-Chung; Chen, Wen-Ming

    2015-02-01

    A bacterial strain designated TNR-22(T) was isolated from a freshwater river in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain TNR-22(T) were facultatively anaerobic, Gram-stain-negative, rod-shaped, motile by a single polar flagellum and formed cream-coloured colonies. Growth occurred at 4-45 °C (optimum, 25-30 °C), with 0-1.0 % (w/v) NaCl (optimum, 0.5 %) and at pH 7.0-8.0 (optimum, pH 7.0). Strain TNR-22(T) did not form nodules on Macroptilium atropurpureum. The nifH gene encoding denitrogenase reductase was not detected by PCR. The major fatty acids (>10 %) of strain TNR-22(T) were C18 : 1ω7c and C16 : 0. The DNA G+C content was 60.3 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, an uncharacterized aminoglycolipid and an uncharacterized phospholipid. Comparative analysis of 16S rRNA gene sequences showed that strain TNR-22(T) constituted a distinct branch within the genus Rhizobium, showing the highest level of sequence similarity with Rhizobium rosettiformans W3(T) (96.3 %). 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 genotypic, chemotaxonomic and phenotypic data, strain TNR-22(T) represents a novel species in the genus Rhizobium, for which the name Rhizobium alvei sp. nov. is proposed. The type strain is TNR-22(T) ( = BCRC 80408(T) = LMG 26895(T) = KCTC 23919(T)).

  16. Rhizobium phaseoli symbiotic mutants with transposon Tn5 insertions.

    PubMed Central

    Noel, K D; Sanchez, A; Fernandez, L; Leemans, J; Cevallos, M A

    1984-01-01

    Rhizobium phaseoli CFN42 DNA was mutated by random insertion of Tn5 from suicide plasmid pJB4JI to obtain independently arising strains that were defective in symbiosis with Phaseolus vulgaris but grew normally outside the plant. When these mutants were incubated with the plant, one did not initiate visible nodule tissue (Nod-), seven led to slow nodule development (Ndv), and two led to superficially normal early nodule development but lacked symbiotic nitrogenase activity (Sna-). The Nod- mutant lacked the large transmissible indigenous plasmid pCFN42d that has homology to Klebsiella pneumoniae nitrogenase (nif) genes. The other mutants had normal plasmid content. In the two Sna- mutants and one Ndv mutant, Tn5 had inserted into plasmid pCFN42d outside the region of nif homology. The insertions of the other Ndv mutants were apparently in the chromosome. They were not in plasmids detected on agarose gels, and, in contrast to insertions on indigenous plasmids, they were transmitted in crosses to wild-type strain CFN42 at the same frequency as auxotrophic markers and with the same enhancement of transmission by conjugation plasmid R68.45. In these Ndv mutants the Tn5 insertions were the same as or very closely linked to mutations causing the Ndv phenotype. However, in two mutants with Tn5 insertions on plasmid pCFN42d, an additional mutation on the same plasmid, rather than Tn5, was responsible for the Sna- or Ndv phenotype. When plasmid pJB4JI was transferred to two other R. phaseoli strains, analysis of symbiotic mutants was complicated by Tn5-containing deleted forms of pJB4JI that were stably maintained. Images PMID:6325385

  17. Bacteroides mobilizable and conjugative genetic elements: antibiotic resistance among clinical isolates.

    PubMed

    Quesada-Gómez, Carlos

    2011-12-01

    The conjugation is one of the most important mechanisms of horizontal gene transfer in prokaryotes, leading to genetic variation within a species and the acquisition of new traits, such as antibiotic resistance. Bacteroides is an obligate anaerobe of the colon and a significant opportunistic pathogen. Antibiotic resistance among Bacteroides spp. is rapidly increasing, largely due to the dissemination of DNA transfer factors (plasmids and transposons) harbored by members of this genus. Transfer factors can be divided into two classes, conjugative and mobilizable. Species of the intestinal Bacteroides have yielded different resistance plasmids, all of which have been intensely studied, the plasmids encode high-level MLS resistance conferred by a conserved erm gene. It has been reported an interesting observation associated with the transfer of several of these types of elements, all of which conferred Tcr and displayed greatly increased transfer efficiency following exposure to tetracycline. Many of the conjugative transposons (CTns) in Bacteroides are related to various genetic elements (such as CTnDOT, CTnERL, NBU and others). CTnDOT carries a tetracycline resistance gene, tetQ, and an erythromycin resistance gene, ermF. Resistance to drugs used to treat Bacteroides infections, such as clindamycin, has also been increasing. These conjugal elements have been found in Bacteroides clinical isolates. Thus, horizontal gene transfer could conceivably have played a role in the rising incidence of resistance in this bacterial group.

  18. Evidence for free-living Bacteroides in Cladophora along the shores of the Great Lakes

    USGS Publications Warehouse

    Whitman, Richard L.; Byappanahalli, Muruleedhara; Spoljaric, Ashley; Przybyla-Kelly, Katarzyna; Shively, Dawn A.; Nevers, Meredith

    2014-01-01

    Bacteroides is assumed to be restricted to the alimentary canal of animals and humans and is considered to be non-viable in ambient environments. We hypothesized that Bacteroides could persist and replicate within beach-stranded Cladophora glomerata mats in southern Lake Michigan, USA. Mean Bacteroides concentration (per GenBac3 Taqman quantitative PCR assay) during summer 2012 at Jeorse Park Beach was 5.2 log calibrator cell equivalents (CCE) g-1 dry weight (dw), ranging from 3.7 to 6.7. We monitored a single beach-stranded mat for 3 wk; bacterial concentrations increased by 1.6 log CCE g-1 dw and correlated significantly with ambient temperature (p = 0.003). Clonal growth was evident, as observed by >99% nucleotide sequence similarity among clones. In in vitro studies, Bacteroides concentrations increased by 5.5 log CCE g-1 after 7 d (27°C) in fresh Cladophora collected from rocks. Partial sequencing of the 16S rRNA gene of 36 clones from the incubation experiment showed highly similar genotypes (≥97% sequence overlap). The closest enteric Bacteroides spp. from the National Center for Biotechnology Information database were only 87 to 91% similar. Genomic similarity, clonality, growth, and persistence collectively suggest that putative, free-living Bacteroides inhabit Cladophora mats of southern Lake Michigan. These findings may have important biological, medical, regulatory, microbial source tracking, and public health implications.

  19. 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

  20. Gene transfer into Solanum tuberosum via Rhizobium spp.

    PubMed

    Wendt, Toni; Doohan, Fiona; Winckelmann, Dominik; Mullins, Ewen

    2011-04-01

    Agrobacterium tumefaciens-mediated transformation (ATMT) is the preferred technique for gene transfer into crops. A major disadvantage of the technology remains the complexity of the patent landscape that surrounds ATMT which restricts its use for commercial applications. An alternative system has been described (Broothaerts et al. in Nature 433:629-633, 2005) detailing the propensity of three rhizobia to transform the model crop Arabidopsis thaliana, the non-food crop Nicotiana tabacum and, at a very low frequency, the monocotyledonous crop Oryza sativa. In this report we describe for the first time the genetic transformation of Solanum tuberosum using the non-Agrobacterium species Sinorhizobium meliloti, Rhizobium sp. NGR234 and Mesorhizobium loti. This was achieved by combining an optimal bacterium and host co-cultivation period with a low antibiotic regime during the callus and shoot induction stages. Using this optimized protocol the transformation frequency (calculated as % of shoots equipped with root systems with the ability to grow in rooting media supplemented with 25 μg/ml hygromycin) of the rhizobia strains was calculated at 4.72, 5.85 and 1.86% for S. meliloti, R. sp. NGR234 and M. loti respectively, compared to 47.6% for the A. tumefaciens control. Stable transgene integration and expression was confirmed via southern hybridisation, quantitative PCR analysis and histochemical screening of both leaf and/or tuber tissue. In light of the rapid advances in potato genomics, combined with the sequencing of the potato genome, the ability of alternative bacteria species to genetically transform this major food crop will provide a novel resource to the Solanaceae community as it continues to develop potato as both a food and non-food crop.

  1. 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.

  2. 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

  3. Humoral immune response to Bacteroides gingivalis fimbrial antigen in mice.

    PubMed Central

    Ogawa, T; Shimauchi, H; Kusumoto, Y; Hamada, S

    1990-01-01

    Bacteroides gingivalis fimbrial antigen incorporated into liposomes, but not in Tris-HCl buffer, significantly raised the levels of anti-fimbriae antibodies in serum, particularly of the IgG class, after oral primary and booster immunizations in BALB/c mice. An approximately linear relationship was observed between the dose of fimbrial antigen and the level of fimbriae-specific antibodies produced; antibody production reached its maximum at an immunization dosage of 500 micrograms of fimbriae per mouse. Fimbriae-specific antibody production was enhanced by use of a semi-synthetic adjuvant, a stearoyl derivative of sodium beta-N-acetylglucosaminyl-(1----4)-N-acetylmuramyl-L-alanyl-D-isoglutaminyl-(L) - stearoyl-(D)-meso-diamino-pimelic acid-(D)-amide-D-alanine (GM)-53) in liposomes. High anti-fimbriae antibody levels in serum and saliva were maintained for several months in the mice that had received two orally administered boosters of fimbrial antigen with GM-53 in liposomes. Salivary anti-fimbriae antibody levels, particularly of the IgA class, were markedly raised. PMID:1968885

  4. Pyogenic arthritis of native joints due to Bacteroides fragilis

    PubMed Central

    Nolla, Joan M.; Murillo, Oscar; Narvaez, Javier; Vaquero, Carmen Gómez; Lora-Tamayo, Jaime; Pedrero, Salvador; Cabo, Javier; Ariza, Javier

    2016-01-01

    Abstract 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

  5. Protective immunization against experimental Bacteroides (Porphyromonas) gingivalis infection.

    PubMed Central

    Chen, P B; Davern, L B; Schifferle, R; Zambon, J J

    1990-01-01

    The effects of immunization in modulating the pathogenesis of Bacteroides (Porphyromonas) gingivalis infection in a murine model system were examined. BALB/c mice were immunized by intraperitoneal injection with B. gingivalis ATCC 53977 (one injection per week for 3 weeks), or with a lithium diiodosalicylate (LIS) extract (one injection per week for 3 weeks), or with lipopolysaccharide (LPS; one intravenous or intraperitoneal injection) from this same strain. Two weeks after the final immunization, the mice were challenged by subcutaneous injection of B. gingivalis ATCC 53977. Mice immunized with bacteria had no secondary lesions and no septicemia, whereas mice immunized with LIS extract had few secondary lesions and no septicemia. Mice immunized with LPS and nonimmunized mice demonstrated secondary abdominal lesions and septicemia after challenge. Bacterial cells and LIS extract, but not LPS, induced serum antibody and antigen reactive lymphocytes, as measured by enzyme-linked immunosorbent assay, immunoblot, Western immunoblot transfer, and in vitro lymphoproliferative responses. The present study suggests that immunization with a LIS extract or whole cells may induce a protective response against experimental B. gingivalis infection. Images PMID:2401568

  6. Metabolism and growth yields in Bacteroides ruminicola strain b14.

    PubMed Central

    Howlett, M R; Mountfort, D O; Turner, K W; Roberton, A M

    1976-01-01

    Metabolism of D-glucose by Bacteroides ruminicola subsp. brevis, strain B14, has been examined. Growth yield studies gave molar growth yields, corrected for storage polysaccharide, of approximately 66 g (dry weight)/mol of glucose fermented. The storage polysaccharide amounted to about 14% of the total dry weight, or 55% of the total cellular carbohydrate, at full growth. After correcting glucose utilization for incorporation into cellular carbohydrate, measurement of product formation showed that 1.1 succinate, 0.8 acetate, and 0.35 formate are produced and 0.5 CO2 net is taken up during the fermentation of 1 glucose under the conditions used. The implication of these results with respect to adenosine 5'-triphosphate (ATP) molar growth yield calculations is discussed. If substrate-level phosphorylation reactions alone are responsible for ATP generation, then the ATP molar growth yield must be about 23 g (dry weight)/mol of ATP. Alternatively, if anaerobic electron transfer-linked phosphorylation also occurs, the ATP molar growth yield will be lower. Images PMID:970946

  7. Superoxide dismutase and O2 lethality in Bacteroides fragilis.

    PubMed Central

    Privalle, C T; Gregory, E M

    1979-01-01

    Exposure of midlog Bacteroides fragils (VPI 2393) to 2% O2-98% N2 caused a three- to fivefold increase in superoxide dismutase specific activity within the cells. The increase in specific activity was completed within 90 min after exposure to oxygen and was dependent upon protein synthesis. Cells containing the higher superoxide dismutase level were more resistant to the effects of 5 atm of oxygen tension than were cells containing the lower level of superoxide dismutase but were equally resistant to 5 atm of nitrogen tension. Similar results were observed upon comparing viability experiments with B. fragilis and B. vulgatus. Superoxide dismutase activity in sonic extracts of B. fragilis was rapidly inactivated by exposure to 5 mM H2O2 and was inhibited by 1 mM NaN3 but not 5 mM NaCN. The inhibition pattern is identical to the pattern demonstrated for the purified iron-containing enzyme from Escherichia coli B and suggests that the superoxide dismutase in B. fragilis is an iron enzyme. PMID:438129

  8. 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

  9. Gene fusion vehicles for the analysis of gene expression in Rhizobium meliloti.

    PubMed Central

    Kahn, M L; Timblin, C R

    1984-01-01

    A set of plasmid cloning vehicles was developed to facilitate the construction of gene or operon fusions in Rhizobium meliloti. The vehicles also contain a broad-host-range replicon and could be introduced into bacteria either by transformation or by transduction, using bacteriophage P2. Insertion of foreign DNA into a unique restriction endonuclease cleavage site promotes the synthesis of either the Escherichia coli lactose operon or the kanamycin phosphotransferase gene from transposon Tn5. Expression of the lactose operon could be detected by observing the color of Rhizobium colonies on medium that contained a chromogenic indicator. We also determined the growth conditions that make it possible to select either for or against the expression of the E. coli lactose operon in R. meliloti. Recombinant plasmids were constructed by inserting MboI restriction fragments of R. meliloti DNA into one of the vehicles, pMK353 . Expression of beta-galactosidase by a number of these recombinants was measured in both R. meliloti and E. coli. PMID:6327625

  10. Genetic and Structural Analysis of the Bacteroides Conjugative Transposon CTn341

    PubMed Central

    Bacic, M.; Parker, A. C.; Stagg, J.; Whitley, H. P.; Wells, W. G.; Jacob, L. A.; Smith, C. J.

    2005-01-01

    The genetic structure and functional organization of a Bacteroides conjugative transposon (CTn), CTn341, were determined. CTn341 was originally isolated from a tetracycline-resistant clinical isolate of Bacteroides vulgatus. The element was 51,993 bp long, which included a 5-bp coupling sequence that linked the transposon ends in the circular form. There were 46 genes, and the corresponding gene products fell into three major functional groups: DNA metabolism, regulation and antibiotic resistance, and conjugation. The G+C content and codon usage observed in the functional groups suggested that the groups belong to different genetic lineages, indicating that CTn341 is a composite, modular element. Mutational analysis of genes representing the different functional groups provided evidence for the gene assignments and showed that the basic conjugation and excision genes are conserved among Bacteroides spp. A group IIA1 intron, designated B.f.I1, was found to be inserted into the bmhA methylase gene. Reverse transcriptase PCR analysis of CTn341 RNA showed that B.fr.I1 was functional and was spliced out of the bmhA gene. Six related CTn-like elements were found in the genome sequences of Bacteroides fragilis NCTC9343 and Bacteroides thetaiotaomicron VPI5482. The putative elements were similar to CTn341 primarily in the tra and mob regions and in the exc gene, and several appeared to contain intron elements. Our data provide the first reported sequence for a complete Bacteroides CTn, and they should be of considerable benefit to further functional and genetic analyses of antibiotic resistance elements and genome evolution in Bacteroides. PMID:15805532

  11. 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.

  12. 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

  13. Identification of a Collagen Type I Adhesin of Bacteroides fragilis

    PubMed Central

    Galvão, Bruna P. G. V.; Weber, Brandon W.; Rafudeen, Mohamed S.; Ferreira, Eliane O.; Patrick, Sheila; Abratt, Valerie R.

    2014-01-01

    Bacteroides fragilis is an opportunistic pathogen which can cause life threatening infections in humans and animals. The ability to adhere to components of the extracellular matrix, including collagen, is related to bacterial host colonisation. Collagen Far Western analysis of the B. fragilis outer membrane protein (OMP) fraction revealed the presence two collagen adhesin bands of ∼31 and ∼34 kDa. The collagen adhesins in the OMP fraction were separated and isolated by two-dimensional SDS-PAGE and also purified by collagen affinity chromatography. The collagen binding proteins isolated by both these independent methods were subjected to tandem mass spectroscopy for peptide identification and matched to a single hypothetical protein encoded by B. fragilis NCTC 9343 (BF0586), conserved in YCH46 (BF0662) and 638R (BF0633) and which is designated in this study as cbp1 (collagen binding protein). Functionality of the protein was confirmed by targeted insertional mutagenesis of the cbp1 gene in B. fragilis GSH18 which resulted in the specific loss of both the ∼31 kDa and the ∼34 kDa adhesin bands. Purified his-tagged Cbp1, expressed in a B. fragilis wild-type and a glycosylation deficient mutant, confirmed that the cbp1 gene encoded the observed collagen adhesin, and showed that the 34 kDa band represents a glycosylated version of the ∼31 kDa protein. Glycosylation did not appear to be required for binding collagen. This study is the first to report the presence of collagen type I adhesin proteins in B. fragilis and to functionally identify a gene encoding a collagen binding protein. PMID:24618940

  14. Metabolism of Tryptophan and Tryptophan Analogs by Rhizobium meliloti1

    PubMed Central

    Williams, Myron N. V.; Signer, Ethan R.

    1990-01-01

    The alfalfa symbiont Rhizobium meliloti Rm1021 produces indole-3-acetic acid in a regulated manner when supplied with exogenous tryptophan. Mutants with altered response to tryptophan analogs still produce indole-3-acetic acid, but are Fix− because bacteria do not fully differentiate into the nitrogen-fixing bacteriod form. These mutations are in apparently essential genes tightly linked to a dominant streptomycin resistance locus. Images Figure 2 PMID:16667364

  15. Rapid synthesis and metabolism of glutamate in N/sub 2/-fixing bacteroids. [Bradyrhizobium japonicum

    SciTech Connect

    Salminen, S.O.; Streeter, J.G.

    1987-04-01

    Symbiotic nodule bacteroids are thought to support N/sub 2/ fixation mainly by metabolizing dicarboxylic acids to CO/sub 2/, generating reductant and ATP required by nitrogenase. Bradyrhizobium japonicum bacteroids were isolated anaerobically and incubated at 2% O/sub 2/ with /sup 14/C-labeled succinate, malate, glutamate, or aspartate. /sup 14/CO/sub 2/ was collected, and the bacteroid contents separated into neutral, organic acid, and amino acid fractions. The respiration of substrates, relative to their uptake, was malate > glutamate > succinate > aspartate. Analysis of the fractions revealed that will all substrates the radioactivity was found mostly in the amino acid fraction. The labeling of the neutral fraction was negligible and only a small amount of label was found in the organic acid fraction indicating a small pool size. TLC of the amino acid fraction showed the label to be principally in glutamate. Glutamate contained 67, 80, 97, and 88% of the /sup 14/C in the amino acid fraction in bacteroids fed with succinate, malate, glutamate and aspartate, respectively. The data suggest that glutamate may play an important role in the bacteroid function.

  16. Bacteroides species from the oral cavity and oral-associated diseases of cats.

    PubMed

    Love, D N; Johnson, J L; Moore, L V

    1989-03-01

    One hundred and sixty-seven strains of Bacteroides were isolated from 71 subcutaneous fight-wound abscesses of cats, 21 cases of feline pyothorax, normal gingival margins from 10 cats and 6 cases of feline gingivitis. Bacteroides species constituted (as a proportion of all anaerobic isolates examined) 44.5% from subcutaneous abscesses, 33.7% from pyothoraxes, 37.5% from normal gingiva and 27.7% from diseased gingiva. Bacteroides tectum comprised 43.7% or 73 of 167 strains, followed by the black- or brown-pigmented asaccharolytic feline species of B. gingivalis, B. salivosus and Group B, comprising 32.3% or 54 of 167 strains. B. heparinolyticus (some 10% or 17 of 167 strains) was the next most common species described. The remainder consisted of two strains of B. fragilis and 21 unspeciated strains. Bacteroides tectum was frequently isolated from subcutaneous abscesses (43.7%) and pyothoraxes (46.6%), and it constituted some 33% of anaerobic isolated from normal gingiva. Bacteroides heparinolyticus was more commonly encountered in purulent lesions (abscesses and pyothoraxes) than in the oral cavity.

  17. Rhizobium pongamiae sp. nov. from root nodules of Pongamia pinnata.

    PubMed

    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-01(T) 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-01(T) has the major cellular fatty acid as C(18:1) ω7c (65.92%). Strain VKLR-01(T) 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-01(T) = (MTCC 10513(T) = MSCL 1015(T)) 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.

  18. 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

  19. Rhizobium rosettiformans sp. nov., isolated from a hexachlorocyclohexane dump site, and reclassification of Blastobacter aggregatus Hirsch and Muller 1986 as Rhizobium aggregatum comb. nov.

    PubMed

    Kaur, Jaspreet; Verma, Mansi; Lal, Rup

    2011-05-01

    A Gram-negative, rod-shaped, motile, aerobic bacterial strain, W3(T), was isolated from hexachlorocyclohexane (HCH)-contaminated groundwater from Lucknow, India, and its taxonomic position was determined using a polyphasic approach. Strain W3(T) shared highest 16S rRNA gene sequence similarity of 97.8 % with Rhizobium selenitireducens B1(T), followed by Rhizobium daejeonense L61(T) (97.7 %), Rhizobium radiobacter ATCC 19358(T) (97.5 %) and Blastobacter aggregatus IFAM 1003(T) (97.2 %). Strain W3(T) formed a monophyletic clade with Blastobacter aggregatus IFAM 1003(T) ( = DSM 1111(T)) in the cluster of species of the genus Rhizobium. Phylogenetic analyses of strain W3(T) using atpD and recA gene sequences confirmed the phylogenetic arrangements obtained by using 16S rRNA gene sequences. Hence, the taxonomic characterization of B. aggregatus DSM 1111(T) was also undertaken. Strains W3(T) and B. aggregatus DSM 1111(T) contained summed feature 8 (18 : 1ω7c and/or 18 : 1ω6c; 65.4 and 70.8 %, respectively) as the major fatty acid, characteristic of the genus Rhizobium. DNA-DNA relatedness of strain W3(T) with Rhizobium selenitireducens LMG 24075(T), Rhizobium daejeonense DSM 17795(T), Rhizobium radiobacter DSM 30147(T) and B. aggregatus DSM 1111(T) was 42, 34, 30 and 34 %, respectively. The DNA G+C contents of strain W3(T) and B. aggregatus DSM 1111(T) were 62.3 and 62.7 mol%, respectively. A nifH gene encoding dinitrogenase reductase was detected in strain W3(T) but not in B. aggregatus DSM 1111(T). Based on the results obtained by phylogenetic and chemotaxonomic analyses, phenotypic characterization and DNA-DNA hybridization, it is concluded that strain W3(T) represents a novel species of the genus Rhizobium, for which the name Rhizobium rosettiformans sp. nov. is proposed (type strain W3(T)  = CCM 7583(T)  = MTCC 9454(T)). It is also proposed that Blastobacter aggregatus Hirsch and Müller 1986 be transferred to the genus Rhizobium as Rhizobium

  20. Identification of fast-growing rhizobia nodulating tropical legumes from Puerto Rico as Rhizobium gallicum and Rhizobium tropici.

    PubMed

    Zurdo-Piñeiro, José Luis; Velázquez, Encarna; Lorite, María José; Brelles-Mariño, Graciela; Schröder, Eduardo C; Bedmar, Eulogio J; Mateos, Pedro F; Martínez-Molina, Eustoquio

    2004-08-01

    Fifteen isolates from several nodulated tropical legumes from Puerto Rico (USA) were characterised by their phenotypic, molecular and symbiotic features. The identification of isolates was based on a polyphasic approach, including phenotypic characteristics, 16S rRNA sequencing, Low molecular weight (LMW) RNA profiles, Two Primers-RAPD patterns, and restriction patterns from 16S rDNA molecules. Despite of the variety of hosts included in this study the 15 isolates were separated into only two groups that corresponded to Rhizobium gallicum and Rhizobium tropici. This work shows that R. gallicum and R. tropici nodulate legume plants, such as Sesbania, Caliandra, Poitea, Piptadenia, Neptunia and Mimosa species, that were not previously considered as hosts for these rhizobia. Moreover, some of these host plants can be nodulated by both species. The results confirm the great promiscuity of R. tropici and also support the hypothesis that the species R. gallicum may be native from America or cosmopolitan and worldwide spread.

  1. Rhizobium pseudoryzae sp. nov., isolated from the rhizosphere of rice.

    PubMed

    Zhang, Xiaoxia; Sun, Lei; Ma, Xiaotong; Sui, Xin Hua; Jiang, Ruibo

    2011-10-01

    A Gram-stain-negative, aerobic, rod-shaped bacterium, designated strain J3-A127(T), was isolated from the roots of fresh rice plants (Oryza sativa). 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 oryzae Alt 505(T) (96.4 %). The low levels of 16S rRNA gene sequence similarity (<90 %) found between the gyrB, atpD, recA and glnII gene sequences of strain J3-A127(T) and the type strains of recognized species of the genus Rhizobium also indicated that it represented a separate species. The temperature range for growth was 10-40 °C (optimum around 28 °C) and the pH range was 6.0-11.0 (optimum pH 7.0-8.0). Strain J3-A127(T) tolerated NaCl concentrations up to 5.0 % (w/v). The strain was catalase- and oxidase-positive. The main cellular fatty acids were summed feature 8 (C(18 : 1)ω7c and/or C(18 : 1)ω6; 46.7 %). The DNA G+C content of strain J3-A127(T) was 59.5 mol%. Strain J3-A127(T) did not form any nodules on four different legumes and the nodD and nifH genes were not detected by PCR. According to physiological and biochemical characteristics and genotypic data, strain J3-A127(T) is considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium pseudoryzae sp. nov. is proposed. The type strain is J3-A127(T) ( = ACCC 10380(T) = KCTC 23294(T)).

  2. 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).

  3. Rhizobium lusitanum sp. nov. a bacterium that nodulates Phaseolus vulgaris.

    PubMed

    Valverde, Angel; Igual, José M; Peix, Alvaro; Cervantes, Emilio; Velázquez, Encarna

    2006-11-01

    The species Phaseolus vulgaris is a promiscuous legume nodulated by several species of the family Rhizobiaceae. During a study of rhizobia nodulating this legume in Portugal, we isolated several strains that nodulate P. vulgaris effectively and also Macroptilium atropurpureum and Leucaena leucocephala, but they form ineffective nodules in Medicago sativa. According to phylogenetic analysis of the 16S rRNA gene sequence, the strains from this study belong to the genus Rhizobium, with Rhizobium rhizogenes and Rhizobium tropici as the closest related species, with 99.9 and 99.2% similarity, respectively, between the type strains of these species and strain P1-7T. The nodD and nifH genes carried by strain P1-7T are phylogenetically related to those of other species nodulating Phaseolus. This strain does not carry virulence genes present in the type strain of R. rhizogenes, ATCC 11325T. Analysis of the recA and atpD genes confirms this phylogenetic arrangement, showing low similarity with respect to those of R. rhizogenes ATCC 11325T (91.9 and 94.1% similarity, respectively) and R. tropici IIB CIAT 899T (90.6% and 91.8% similarity, respectively). The intergenic spacer (ITS) of the strains from this study is phylogenetically divergent from those of R. rhizogenes ATCC 11235T and R. tropici CIAT 899T, with 85.9 and 82.8% similarity, respectively, with respect to strain P1-7T. The tRNA profile and two-primer random amplified polymorphic DNA pattern of strain P1-7T are also different from those of R. rhizogenes ATCC 11235T and R. tropici CIAT 899T. The strains isolated in this study can be also differentiated from R. rhizogenes and R. tropici by several phenotypic characteristics. The results of DNA-DNA hybridization showed means of 28 and 25% similarity between strain P1-7T and R. rhizogenes ATCC 11235T and R. tropici CIAT 899T, respectively. All these data showed that the strains isolated in this study belong to a novel species of the genus Rhizobium, for which we propose

  4. Differential growth of bowel commensal Bacteroides species on plant xylans of differing structural complexity.

    PubMed

    Centanni, Manuela; Hutchison, Jennifer C; Carnachan, Susan M; Daines, Alison M; Kelly, William J; Tannock, Gerald W; Sims, Ian M

    2017-02-10

    Alterations to the composition of the bowel microbiota (dysbioses) are associated with particular diseases and conditions of humans. There is a need to discover new, indigestible polysaccharides which are selective growth substrates for commensal bowel bacteria. These substrates (prebiotics) could be added to food in intervention studies to correct bowel dysbiosis. A collection of commensal bacteria was screened for growth in culture using a highly-branched xylan produced by New Zealand flax. Two, Bacteroides ovatus ATCC 8483 and Bacteroides xylanisolvens DSM 18836 grew well on this substrate. The utilisation of the xylan was studied chromatographically and by constituent sugar analysis. The two closely related species utilised the xylan in different ways, and differently from their use of wheat arabinoxylan. The growth of Bacteroides species on other plant xylans having differing chemical structures was also investigated. Novel xylans expand the choice of potential prebiotics that could be used to correct bowel dysbioses.

  5. 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.

  6. Cloning of a Bacteroides fragilis chromosomal determinant coding for 5-nitroimidazole resistance.

    PubMed

    Haggoud, A; Reysset, G; Sebald, M

    1992-08-01

    Strain BF8 is a plasmid-free Bacteroides fragilis, resistant to 5-nitroimidazole (5-Ni) antibiotics (metronidazole, ornidazole and tinidazole). The resistance was transferable by conjugation into Bacteroides fragilis BF638R. The total DNA of a Nir transconjugant was used for the construction of a Sau3A genomic library in a B. fragilis cloning vector pFK707 delta H1 (4.2 kb). By electrotransformation of strain BF638R, a recombinant plasmid containing an insert of 5.4 kb was obtained which conferred to the host strain the resistance to 5-Ni. The physical map of the insert was established. After deletion analysis of the insert, the Nir determinant was localized on a HpaII-HincII fragment of 1.6 kb in size. This Nir determinant has been compared by Southern-blot analysis with other Bacteroides Nir determinants of plasmid origin.

  7. Novel Bacteroides host strains for detection of human- and animal-specific bacteriophages in water.

    PubMed

    Wicki, Melanie; Auckenthaler, Adrian; Felleisen, Richard; Tanner, Marcel; Baumgartner, Andreas

    2011-03-01

    Bacteriophages active against specific Bacteroides host strains were shown to be suitable for detection of human faecal pollution. However, the practical application of this finding is limited because some specific host strains were restricted to certain geographic regions. In this study, novel Bacteroides host strains were isolated that discriminate human and animal faecal pollution in Switzerland. Two strains specific for bacteriophages present in human faecal contamination and three strains specific for bacteriophages indicating animal faecal contamination were evaluated. Bacteriophages infecting human strains were exclusively found in human wastewater, whereas animal strains detected bacteriophages only in animal waste. The newly isolated host strains could be used to determine the source of surface and spring water faecal contamination in field situations. Applying the newly isolated host Bacteroides thetaiotaomicron ARABA 84 for detection of bacteriophages allowed the detection of human faecal contamination in spring water.

  8. Bacteremia due to Bacteroides fragilis after elective appendectomy in renal transplant recipients.

    PubMed

    Fisher, M C; Baluarte, H J; Long, S S

    1981-05-01

    Bacteremia caused by Bacteroides fragilis occurred in four of 75 children after renal transplantation, and B. fragilis was the most common cause of postoperative bacteremia. Bacteroides bacteremia was significantly associated with performance of elective appendectomy at the time of transplantation (P less than 0.01) and with profound lymphocytopenia (P = 0.01). No patient received antibiotics at the time of surgery or prior to the first positive blood culture, yet B. fragilis was the single organism isolated from blood and abscesses in these patients. A role for lymphocytes in containment of B. fragilis has not been suggested previously, although unexplained occurrence of bacteroides bacteremia in immunocompromised patients has occasionally been reported. Lymphocytes themselves may be important in this host-bacterium interaction, or lymphocytopenia may be the marker for a more generalized deficiency in host defenses.

  9. Colonization with enterotoxigenic Bacteroides fragilis is associated with early-stage colorectal neoplasia

    PubMed Central

    Pearson, John; Aitchison, Alan; Dixon, Liane; Frizelle, Frank A.; Keenan, Jacqueline I.

    2017-01-01

    Background Enterotoxigenic Bacteroides fragilis (ETBF) is a toxin-producing bacteria thought to possibly promote colorectal carcinogenesis by modulating the mucosal immune response and inducing epithelial cell changes. Here, we aim to examine the association of colonic mucosal colonization with ETBF and the presence of a range of lesions on the colonic neoplastic spectrum. Methods Mucosal tissue from up to four different colonic sites was obtained from a consecutive series of 150 patients referred for colonoscopy. The presence and relative abundance of the B. fragilis toxin gene (bft) in each tissue sample was determined using quantitative PCR, and associations with clinicopathological characteristics were analysed. Findings We found a high concordance of ETBF between different colonic sites (86%). Univariate analysis showed statistically significant associations between ETBF positivity and the presence of low-grade dysplasia (LGD), tubular adenomas (TA), and serrated polyps (P-values of 0.007, 0.027, and 0.007, respectively). A higher relative abundance of ETBF was significantly associated with LGD and TA (P-values of < 0.0001 and 0.025, respectively). Increased ETBF positivity and abundance was also associated with left-sided biopsies, compared to those from the right side of the colon. Conclusion Our results showing association of ETBF positivity and increased abundance with early-stage carcinogenic lesions underlines its importance in the development of colorectal cancer, and we suggest that detection of ETBF may be a potential marker of early colorectal carcinogenesis. PMID:28151975

  10. Comparison of standard, quantitative and digital PCR in the detection of enterotoxigenic Bacteroides fragilis.

    PubMed

    Purcell, Rachel V; Pearson, John; Frizelle, Frank A; Keenan, Jacqueline I

    2016-09-30

    Gut colonization with enterotoxigenic Bacteroides fragilis (ETBF) appears to be associated with the development of colorectal cancer. However, differences in carriage rates are seen with various testing methods and sampling sites. We compared standard PCR, SYBR green and TaqMan quantitative PCR (qPCR) and digital PCR (dPCR) in detecting the B. fragilis toxin (bft) gene from cultured ETBF, and from matched luminal and faecal stool samples from 19 colorectal cancer patients. Bland-Altman analysis found that all three quantitative methods performed comparably in detecting bft from purified bacterial DNA, with the same limits of detection (<1 copy/μl). However, SYBR qPCR under-performed compared to TaqMan qPCR and dPCR in detecting bft in clinical stool samples; 13/38 samples were reported positive by SYBR, compared to 35 and 36 samples by TaqMan and dPCR, respectively. TaqMan qPCR and dPCR gave bft copy numbers that were 48-fold and 75-fold higher for the same samples than SYBR qPCR, respectively (p < 0.001). For samples that were bft-positive in both fecal and luminal stools, there was no difference in relative abundance between the sites, by any method tested. From our findings, we recommend the use of TaqMan qPCR as the preferred method to detect ETBF from clinical stool samples.

  11. 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.

  12. Bacteroides dorei dominates gut microbiome prior to autoimmunity in Finnish children at high risk for type 1 diabetes.

    PubMed

    Davis-Richardson, Austin G; Ardissone, Alexandria N; Dias, Raquel; Simell, Ville; Leonard, Michael T; Kemppainen, Kaisa M; Drew, Jennifer C; Schatz, Desmond; Atkinson, Mark A; Kolaczkowski, Bryan; Ilonen, Jorma; Knip, Mikael; Toppari, Jorma; Nurminen, Noora; Hyöty, Heikki; Veijola, Riitta; Simell, Tuula; Mykkänen, Juha; Simell, Olli; Triplett, Eric W

    2014-01-01

    The incidence of the autoimmune disease, type 1 diabetes (T1D), has increased dramatically over the last half century in many developed countries and is particularly high in Finland and other Nordic countries. Along with genetic predisposition, environmental factors are thought to play a critical role in this increase. As with other autoimmune diseases, the gut microbiome is thought to play a potential role in controlling progression to T1D in children with high genetic risk, but we know little about how the gut microbiome develops in children with high genetic risk for T1D. In this study, the early development of the gut microbiomes of 76 children at high genetic risk for T1D was determined using high-throughput 16S rRNA gene sequencing. Stool samples from children born in the same hospital in Turku, Finland were collected at monthly intervals beginning at 4-6 months after birth until 2.2 years of age. Of those 76 children, 29 seroconverted to T1D-related autoimmunity (cases) including 22 who later developed T1D, the remaining 47 subjects remained healthy (controls). While several significant compositional differences in low abundant species prior to seroconversion were found, one highly abundant group composed of two closely related species, Bacteroides dorei and Bacteroides vulgatus, was significantly higher in cases compared to controls prior to seroconversion. Metagenomic sequencing of samples high in the abundance of the B. dorei/vulgatus group before seroconversion, as well as longer 16S rRNA sequencing identified this group as Bacteroides dorei. The abundance of B. dorei peaked at 7.6 months in cases, over 8 months prior to the appearance of the first islet autoantibody, suggesting that early changes in the microbiome may be useful for predicting T1D autoimmunity in genetically susceptible infants. The cause of increased B. dorei abundance in cases is not known but its timing appears to coincide with the introduction of solid food.

  13. 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...

  14. 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-...

  15. 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

  16. Cephalosporinases associated with outer membrane vesicles released by Bacteroides spp. protect gut pathogens and commensals against β-lactam antibiotics

    PubMed Central

    Stentz, Régis; Horn, Nikki; Cross, Kathryn; Salt, Louise; Brearley, Charles; Livermore, David M.; Carding, Simon R.

    2015-01-01

    Objectives To identify β-lactamase genes in gut commensal Bacteroides species and to assess the impact of these enzymes, when carried by outer membrane vesicles (OMVs), in protecting enteric pathogens and commensals. Methods A deletion mutant of the putative class A β-lactamase gene (locus tag BT_4507) found in the genome of the human commensal Bacteroides thetaiotaomicron was constructed and a phenotypic analysis performed. A phylogenetic tree was built from an alignment of nine Bacteroides cephalosporinase protein sequences, using the maximum likelihood method. The rate of cefotaxime degradation after incubation with OMVs produced by different Bacteroides species was quantified using a disc susceptibility test. The resistance of Salmonella Typhimurium and Bifidobacterium breve to cefotaxime in liquid culture in the presence of B. thetaiotaomicron OMVs was evaluated by measuring bacterial growth. Results The B. thetaiotaomicron BT_4507 gene encodes a β-lactamase related to the CepA cephalosporinase of Bacteroides fragilis. OMVs produced by B. thetaiotaomicron and several other Bacteroides species, except Bacteroides ovatus, carried surface-associated β-lactamases that could degrade cefotaxime. β-Lactamase-harbouring OMVs from B. thetaiotaomicron protected Salmonella Typhimurium and B. breve from an otherwise lethal dose of cefotaxime. Conclusions The production of membrane vesicles carrying surface-associated β-lactamases by Bacteroides species, which constitute a major part of the human colonic microbiota, may protect commensal bacteria and enteric pathogens, such as Salmonella Typhimurium, against β-lactam antibiotics. PMID:25433011

  17. Evidence for T Cell-dependent Immunity to Bacteroides fragilis in an Intraabdominal Abscess Model

    PubMed Central

    Onderdonk, Andrew B.; Markham, Richard B.; Zaleznik, Dori F.; Cisneros, Ronald L.; Kasper, Dennis L.

    1982-01-01

    It has been shown that active immunization of rats with the capsular polysaccharide of Bacteroides fragilis protects these animals against abscess development following intraperitoneal challenge with this species. Passive transfer of hyperimmune globulin from immunized animals to nonimmune recipients provided protection against B. fragilis bacteremia in challenged animals, but did not confer protection against abscess development. On the other hand, adoptive transfer of spleen cells from immunized animals to nonimmunized recipients resulted in protection against abscesses following challenge with B. fragilis. These data suggested that a T cell-dependent immune response was involved in protection against abscess development after immunization with B. fragilis capsular antigen. To determine the possible role of cell-mediated immunity prompted by the capsular antigen, inbred congenitally athymic OLA/Rnu rats and their phenotypically normal littermates were actively immunized. Despite the development of high titers of anti-B. fragilis capsular antibody, 100% of actively immunized athymic rats developed abscesses, as did 100% of unimmunized athymic control rats. However, no phenotypically normal littermate control rats that were actively immunized developed abscesses, while 100% of phenotypically normal unimmunized rats developed abscesses. Additional studies showed that adoptive transfer of T cell-enriched spleen cell preparations from Wistar/Lewis rats immunized with the capsular polysaccharide to nonimmune recipients also resulted in protection against B. fragilis-induced abscesses. We conclude that the protection afforded by immunization with B. fragilis capsule against intraabdominal abscesses caused by that organism is T cell-mediated and does not require the presence of serum antibody. PMID:6976357

  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. Identification of a gene linked to Rhizobium meliloti ntrA whose product is homologous to a family to ATP-binding proteins.

    PubMed Central

    Albright, L M; Ronson, C W; Nixon, B T; Ausubel, F M

    1989-01-01

    The ntrA gene of Rhizobium meliloti has recently been identified and shown to be required for a diverse set of metabolic functions (C. W. Ronson, B. T. Nixon, L. M. Albright, and F. M. Ausubel, J. Bacteriol. 169:2424-2431, 1987). As a result of sequencing the ntrA gene and its flanking regions from R. meliloti, we identified an open reading frame directly upstream of ntrA, ORF1, whose predicted product is homologous to a superfamily of ATP-binding proteins involved in transport, cell division, nodulation, and DNA repair. The homology of ORF1 to this superfamily and its proximity to ntrA led us to investigate its role in symbiosis by mutagenesis and expression studies. We were unable to isolate an insertion mutation in ORF1, suggesting that ORF1 may code for an essential function. We identified the start of transcription for the ntrA gene in vegetative cells and bacteroids and showed that ORF1 and ntrA are transcriptionally unlinked. ORF1 appears to be in an operon with one or more upstream genes. Images PMID:2703463

  20. A closer look at bacteroides: phylogenetic relationship and genomic implications of a life in the human gut.

    PubMed

    Karlsson, Fredrik H; Ussery, David W; Nielsen, Jens; Nookaew, Intawat

    2011-04-01

    The human gut is extremely densely inhabited by bacteria mainly from two phyla, Bacteroidetes and Firmicutes, and there is a great interest in analyzing whole-genome sequences for these species because of their relation to human health and disease. Here, we do whole-genome comparison of 105 Bacteroidetes/Chlorobi genomes to elucidate their phylogenetic relationship and to gain insight into what is separating the gut living Bacteroides and Parabacteroides genera from other Bacteroidetes/Chlorobi species. A comprehensive analysis shows that Bacteroides species have a higher number of extracytoplasmic function σ factors (ECF σ factors) and two component systems for extracellular signal transduction compared to other Bacteroidetes/Chlorobi species. A whole-genome phylogenetic analysis shows a very little difference between the Parabacteroides and Bacteroides genera. Further analysis shows that Bacteroides and Parabacteroides species share a large common core of 1,085 protein families. Genome atlases illustrate that there are few and only small unique areas on the chromosomes of four Bacteroides/Parabacteroides genomes. Functional classification to clusters of othologus groups show that Bacteroides species are enriched in carbohydrate transport and metabolism proteins. Classification of proteins in KEGG metabolic pathways gives a detailed view of the genome's metabolic capabilities that can be linked to its habitat. Bacteroides pectinophilus and Bacteroides capillosus do not cluster together with other Bacteroides species, based on analysis of 16S rRNA sequence, whole-genome protein families and functional content, 16S rRNA sequences of the two species suggest that they belong to the Firmicutes phylum. We have presented a more detailed and precise description of the phylogenetic relationships of members of the Bacteroidetes/Chlorobi phylum by whole genome comparison. Gut living Bacteroides have an enriched set of glycan, vitamin, and cofactor enzymes important for

  1. Functional characterization of aroA from Rhizobium leguminosarum with significant glyphosate tolerance in transgenic Arabidopsis.

    PubMed

    Han, Jing; Tian, Yong-Sheng; Xu, Jing; Wang, Li-Juan; Wang, Bo; Peng, Ri-He; Yao, Quan-Hong

    2014-09-01

    Glyphosate is the active component of the top-selling herbicide, the phytotoxicity of which is due to its inhibition of the shikimic acid pathway. 5-Enolpyruvylshikimate-3-phosphate synthase (EPSPS) is a key enzyme in the shikimic acid pathway. Glyphosate tolerance in plants can be achieved by the expression of a glyphosate-insensitive aroA gene (EPSPS). In this study, we used a PCR-based two-step DNA synthesis method to synthesize a new aroA gene (aroAR. leguminosarum) from Rhizobium leguminosarum. In vitro glyphosate sensitivity assays showed that aroAR. leguminosarum is glyphosate tolerant. The new gene was then expressed in E. coli and key kinetic values of the purified enzyme were determined. Furthermore, we transformed the aroA gene into Arabidopsis thaliana by the floral dip method. Transgenic Arabidopsis with the aroAR. leguminosarum gene was obtained to prove its potential use in developing glyphosate-resistant crops.

  2. 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.

  3. Induction of interleukin-1 and -6 in human gingival fibroblast cultures stimulated with Bacteroides lipopolysaccharides.

    PubMed Central

    Takada, H; Mihara, J; Morisaki, I; Hamada, S

    1991-01-01

    Normal human gingival fibroblasts stimulated in vitro by lipopolysaccharides (LPS) from oral Bacteroides species produced cell-free and cell-associated thymocyte-activating factors (TAF). Neutralization assays using antisera to human interleukin-1 alpha (HuIL-1 alpha), HuIL-1 beta, and HuIL-6 revealed that cell-free TAF was attributable mainly to IL-1 beta and that IL-6 augmented the TAF activity of IL-1 beta in the culture supernatant. Another factor(s), however, may also be involved in cell-free TAF. By contrast, the active entity of cell-associated TAF was ascribed to IL-1 alpha alone. Furthermore, IL-6 was detected mainly in the supernatant of fibroblast cultures stimulated with Bacteroides LPS. Fibroblasts pretreated with natural human beta or gamma interferon, but not those pretreated with alpha interferon, synthesized higher levels of cell-associated IL-1 alpha in response to stimulation by Bacteroides LPS; however, no interferons exhibited direct IL-1-inducing activity or synergistic IL-1-inducing activity with LPS. Endogenously induced beta interferon was suggested to be necessary for fibroblasts to produce cell-associated IL-1 alpha in response to Bacteroides LPS. PMID:1702762

  4. Immune response to Bacteroides ureolyticus in a patient with brain abscess.

    PubMed Central

    Lalitha, M K; Mathai, K V; Koshi, G

    1983-01-01

    A high titer (1:256) of agglutinating antibodies against Bacteroides ureolyticus was demonstrated in a 35-year-old woman with brain abscess, using a microagglutination test. Tests done with B. ureolyticus and heterologous sera as well as with heterologous strains and the patient's serum were negative. Circulating antibody to B. ureolyticus has not been reported previously. PMID:6619293

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

    DOE PAGES

    Dassa, Bareket; Utturkar, Sagar M.; Hurt, Richard A.; ...

    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.

  6. Genome sequence of the Bacteroides fragilis phage ATCC 51477-B1

    PubMed Central

    Hawkins, Shawn A; Layton, Alice C; Ripp, Steven; Williams, Dan; Sayler, Gary S

    2008-01-01

    The genome of a fecal pollution indicator phage, Bacteroides fragilis ATCC 51477-B1, was sequenced and consisted of 44,929 bases with a G+C content of 38.7%. Forty-six putative open reading frames were identified and genes were organized into functional clusters for host specificity, lysis, replication and regulation, and packaging and structural proteins. PMID:18710568

  7. Growth inhibitory effects of endotoxins from Bacteroides gingivalis and intermedius on human gingival fibroblasts in vitro

    SciTech Connect

    Layman, D.L.; Diedrich, D.L.

    1987-06-01

    Purified endotoxin or lipopolysaccharide from Bacteroides gingivalis and Bacteroides intermedius caused a similar dose-dependent inhibition of growth of cultured human gingival fibroblasts as determined by /sup 3/H-thymidine incorporation and direct cell count. Approximately 200 micrograms/ml endotoxin caused a 50% reduction in /sup 3/H-thymidine uptake of logarithmically growing cells. Inhibition of growth was similar in cultures of fibroblasts derived from either healthy or diseased human gingiva. When examining the change in cell number with time of exposure in culture, the rate of proliferation was significantly suppressed during the logarithmic phase of growth. However, the cells recovered so that the rate of proliferation, although reduced, was sufficient to produce a cell density similar to the control cells with prolonged culture. The endotoxins were characterized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The profiles of the Bacteroides endotoxins were different. B. gingivalis endotoxin showed a wide range of distinct bands indicating a heterogeneous distribution of molecular species. Endotoxin from B. intermedius exhibited a few discrete low molecular weight bands, but the majority of the lipopolysaccharides electrophoresed as a diffuse band of high molecular weight material. The apparent heterogeneity of the two Bacteroides endotoxins and the similarity in growth inhibitory capacity suggest that growth inhibitory effects of these substances cannot be attributed to any polysaccharide species of endotoxin.

  8. 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.

  9. In vitro kinetic analysis of oligofructose consumption by Bacteroides and Bifidobacterium spp. indicates different degradation mechanisms.

    PubMed

    Van der Meulen, Roel; Makras, Lefteris; Verbrugghe, Kristof; Adriany, Tom; De Vuyst, Luc

    2006-02-01

    The growth of pure cultures of Bacteroides thetaiotaomicron LMG 11262 and Bacteroides fragilis LMG 10263 on fructose and oligofructose was examined and compared to that of Bifidobacterium longum BB536 through in vitro laboratory fermentations. Gas chromatography (GC) analysis was used to determine the different fractions of oligofructose and their degradation during the fermentation process. Both B. thetaiotaomicron LMG 11262 and B. fragilis LMG 10263 were able to grow on oligofructose as fast as on fructose, succinic acid being the major metabolite produced by both strains. B. longum BB536 grew slower on oligofructose than on fructose. Acetic acid and lactic acid were the main metabolites produced when fructose was used as the sole energy source. Increased amounts of formic acid and ethanol were produced when oligofructose was used as an energy source at the cost of lactic acid. Detailed kinetic analysis revealed a preferential metabolism of the short oligofructose fractions (e.g., F2 and F3) for B. longum BB536. After depletion of the short fractions, the larger oligofructose fractions (e.g., F4, GF4, F5, GF5, and F6) were metabolized, too. Both Bacteroides strains did not display such a preferential metabolism and degraded all oligofructose fractions simultaneously, transiently increasing the fructose concentration in the medium. This suggests a different mechanism for oligofructose breakdown between the strain of Bifidobacterium and both strains of Bacteroides, which helps to explain the bifidogenic nature of inulin-type fructans.

  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. Method for Testing Degree of Infectivity of Rhizobium meliloti Strains.

    PubMed

    Olivares, J; Casadesús, J; Bedmar, E J

    1980-05-01

    The infectiveness of different strains of Rhizobium meliloti was tested with a technique that uses the addition of tetracycline to the root medium. To stop the infection, the antibiotic was added some time after the inoculation of Medicago sativa plants. A coefficient of infectivity for each strain was calculated according to the number of nodules that appeared with and without the addition of the antibiotic. This method seems useful in infectivity studies and is simpler and easier to perform than the test of competence between strains.

  12. 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

  13. Method for Testing Degree of Infectivity of Rhizobium meliloti Strains

    PubMed Central

    Olivares, José; Casadesús, Josep; Bedmar, Eulogio J.

    1980-01-01

    The infectiveness of different strains of Rhizobium meliloti was tested with a technique that uses the addition of tetracycline to the root medium. To stop the infection, the antibiotic was added some time after the inoculation of Medicago sativa plants. A coefficient of infectivity for each strain was calculated according to the number of nodules that appeared with and without the addition of the antibiotic. This method seems useful in infectivity studies and is simpler and easier to perform than the test of competence between strains. PMID:16345574

  14. Effect of Salinity on Rhizobium Growth and Survival †

    PubMed Central

    Singleton, P. W.; El Swaify, S. A.; Bohlool, B. B.

    1982-01-01

    This study examines the effect of salinity on the growth and survival of Rhizobium spp. in culture media and soil. Eleven isolates from saline and nonsaline environments were compared. The growth (mean doubling time) of all strains and species tested decreased when the electrical conductivity of the culture medium (yeast extract-mannitol) was raised from 1.2 mS cm−1 to 6.7 mS cm−1 (15% seawater equivalent) or to 13.1 mS cm−1 (28% seawater equivalent). Three of eleven strains failed to grow at 13.1 mS cm−1. Although growth was affected by salinity, four strains selected from the growth rate study could survive in extremely high concentrations of salt. Two strains with growth rates sensitive to salt and two strains with growth rates relatively unaffected by salt were inoculated into solutions with electrical conductivities of up to 43.0 mS cm−1 (92% seawater equivalent). Not only did all four strains survive the initial osmotic shock (at 5 h after inoculation), but it was not until 27 days after inoculation that the sensitive strains exhibited a significant reduction in viable numbers. The salt-tolerant strains survived for more than 65 days with no reduction in viable counts. The interaction between soil moisture tension and soil salinity in relation to Rhizobium survival in gamma-irradiated soil was also examined. Six treatment combinations were used, ranging from −0.1 bars and 0.2 mS cm−1 to −15 bars and 12 mS cm−1. Sensitive strains declined from 107 to 105 organisms per g of soil after 84 days of incubation at −15 bars and 12 mS cm−1. Tolerant strains survived for the same period with no loss in viable numbers. The results of these experiments indicate that many strains of Rhizobium can grow and survive at salt concentrations which are inhibitory to most agricultural legumes. The emphasis of research concerning the effects of salinity on symbiotic nitrogen fixation should, therefore, be directed to aspects of the symbiosis other than the

  15. Lower Level of Bacteroides in the Gut Microbiota Is Associated with Inflammatory Bowel Disease: A Meta-Analysis

    PubMed Central

    Zhou, Yingting

    2016-01-01

    Background and Aims. Multiple studies have reported associations between inflammatory bowel disease (IBD) and the flora disequilibrium of Bacteroides. We performed a meta-analysis of the available data to provide a more precise estimate of the association between Bacteroides level in the gut and IBD. Methods. We searched PubMed/MEDLINE, EMBASE, Cochrane Library, Wiley Library, BIOSIS previews, Web of Science, CNKI, and ScienceDirect databases for published literature on IBD and gut microbiota from 1990 to 2016. Quality of all eligible studies was assessed using the Newcastle-Ottawa Quality Assessment Scale (NOS). We compared the level of Bacteroides in IBD patients with that in a control group without IBD, different types of IBD patients, and IBD patients with active phase and in remission. Results. We identified 63 articles, 9 of which contained sufficient data for evaluation. The mean level of Bacteroides was significantly lower in Crohn's disease (CD) and ulcerative colitis (UC) patients in active phase than in normal controls. The level of Bacteroides in remission CD and UC patients was much lower than patients in the control group. Bacteroides level was even lower in patients with CD and UC in active phase than in remission. Conclusions. This analysis suggests that lower levels of Bacteroides are associated with IBD, especially in active phase. PMID:27999802

  16. Rhizobium pakistanensis sp. nov., isolated from groundnut (Arachis hypogaea) nodules grown in rainfed Pothwar, Pakistan.

    PubMed

    Khalid, Rabia; Zhang, Yu Jing; Ali, Safdar; Sui, Xin Hua; Zhang, Xiao Xia; Amara, Ummay; Chen, Wen Xin; Hayat, Rifat

    2015-01-01

    A Gram-negative, white, non-motile, rod shaped bacterial strain BN-19(T) was isolated from a root nodule of groundnut (Arachis hypogaea) in Pakistan. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain BN-19(T) formed a subclade in the genus Rhizobium together with Rhizobium alkalisoli CCBAU 01393(T), Rhizobium vignae CCBAU 05176(T), Rhizobium huautlense SO2(T) and Rhizobium tarimense PL-41(T) with sequence similarities of 97.5, 97.3, 97.2 and 97.1 % respectively. Sequence analysis of housekeeping genes atpD, glnII and recA (with sequence similarities of ≤92 %) confirmed the unique position of BN-19(T) in the genus Rhizobium. DNA-DNA relatedness between the strain BN-19(T) and R. alkalisoli CCBAU 01393(T), R. vignae CCBAU 05176(T), R. huautlense SO2(T) and R. tarimense PL-41(T) were 20.6, 22.5, 15.9 and 20.5 % respectively, further confirming that BN-19(T) represents a novel species in the genus Rhizobium. The DNA G + C content was 60.1 mol%. The dominant fatty acids of strain BN-19(T) were C19:0 cyclo ω8c, summed feature 2 (C14:0 3OH and/or C16:1 iso I) and summed feature 8 (C18:1 ω7c). Some phenotypic features also differentiate the strain BN-19(T) from the related species. On the basis of these results, strain BN-19(T) is considered to represent a novel species in the genus Rhizobium, for which the name Rhizobium pakistanensis sp. nov. is proposed. The type strain is BN-19(T) (=LMG 27895(T) = CCBAU 101086(T)).

  17. 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

  18. Genetic structure of a soil population of nonsymbiotic Rhizobium leguminosarum.

    PubMed Central

    Segovia, L; Piñero, D; Palacios, R; Martínez-Romero, E

    1991-01-01

    The genetic structure of a population of nonsymbiotic Rhizobium leguminosarum strains was determined by the electrophoretic mobilities of eight metabolic enzymes. Nonsymbiotic strains were isolated from the rhizosphere of bean plants and characterized by growth on differential media and at different temperatures, intrinsic antibiotic resistance, the lack of homology to a nifH probe, and their inability to form nodules on bean roots. All the isolates clustered with R. leguminosarum bv. phaseoli reference strains and did not encompass any other Rhizobium taxa. Their rRNA operon restriction fragment length polymorphisms and the nucleotide sequence of a fragment of the 16S rRNA gene were also found to be identical to those of R. leguminosarum bv. phaseoli reference strains. When complemented with an R. leguminosarum bv. phaseoli symbiotic plasmid (p42d), the nonsymbiotic isolates were able to fix nitrogen in symbiosis with bean roots at levels similar to those of the parental strain. The symbiotic isolates were found at a relative frequency of 1 in 40 nonsymbiotic R. leguminosarum strains. Images PMID:1707606

  19. Effect of environmental pH on enzyme activity and growth of Bacteroides gingivalis W50.

    PubMed Central

    McDermid, A S; McKee, A S; Marsh, P D

    1988-01-01

    Since the pH of the gingival crevice increases from below neutrality in health to above pH 8 in disease, we decided to investigate the effect of environmental pH on the growth and enzyme activity of Bacteroides gingivalis W50. Cells were grown in a chemostat under hemin-excess conditions over a range of pH values; stable growth was observed only between pH 6.7 and 8.3, with the maximum yields obtained between pH 7.0 and 8.0. The enzyme profile of cells varied markedly with pH. Enzymes with a specificity for gingival connective tissue (collagenase, hyaluronidase) were produced optimally at or below neutral pH, whereas trypsinlike activity increased with the growth pH and was maximal at pH 8.0. Chymotrypsinlike activity was generally low, although its activity was highest at the extremes of growth pH, i.e., at pH 6.7 and 8.3. Inhibitor studies provided evidence that the breakdown of collagen involved the concerted action of both a collagenase and the trypsinlike enzyme. The ratio of trypsin to collagenolytic activity rose from 1:1 during growth at neutral pH and below to almost 7:1 during growth at pH 8.3. Thus B. gingivalis appears to be uniquely adapted as a periodontopathic organism in that under environmental conditions likely to prevail during the initial stages of pocket development it produces maximally those enzymes with a tissue-damaging potential. Then, as the pH of the pocket rises during the host inflammatory response, the activity of the trypsinlike enzyme increases markedly, which may enable cells to inactivate key components of the host defenses such as immunoglobulins and complement. PMID:3281900

  20. Preferential packing of acidic glycosidases and proteases into Bacteroides outer membrane vesicles.

    PubMed

    Elhenawy, Wael; Debelyy, Mykhaylo O; Feldman, Mario F

    2014-03-11

    Outer membrane vesicles (OMV) are spherical membranous structures released from the outer membrane (OM) of Gram-negative bacteria. OMV have been proposed to play several different roles during both pathogenesis and symbiosis. Despite the fact that OMV were described several decades ago, their biogenesis is a poorly characterized process. Whether OMV are produced by an active mechanism or by passive disintegration of the OM is a still matter of controversy. Bacteroides fragilis and Bacteroides thetaiotaomicron are important members of the human microbiota. In this work, we determined and compared the protein compositions of OM and OMV from B. fragilis and B. thetaiotaomicron. SDS-PAGE analysis of both fractions revealed dramatically different protein profiles. Proteomic analysis of OM and OMV in B. fragilis identified more than 40 proteins found exclusively in OMV and more than 30 proteins detectable only in the OM. The OMV-specific proteome showed a high prevalence of glycosidases and proteases, some of which were shown to be active in vitro. Similar results were obtained for B. thetaiotaomicron. Most of the OMV-exclusive proteins were acidic. Based on these results, we propose that these species possess machinery devoted to selectively pack acidic proteins into the OMV. These OMV equipped with hydrolytic enzymes could help in securing nutrients for the benefit of the whole bacterial community present in the microbiota, uncovering a novel function for bacterial OMV. IMPORTANCE The members of genus Bacteroides are key players in the symbiosis between the human host and the gut microbiota. It is known for its ability to degrade a wide variety of glycans that are not substrates for human glycosidases. The cleaved glycans can be utilized by Bacteroides and other microbiota members, resulting in the production of short-chain fatty acids that are beneficial for the host. Although members of the genus Bacteroides are known to secrete different hydrolases, their secretion

  1. Rhizobium favelukesii sp. nov., isolated from the root nodules of alfalfa (Medicago sativa L).

    PubMed

    Torres Tejerizo, Gonzalo; Rogel, Marco Antonio; Ormeño-Orrillo, Ernesto; Althabegoiti, María Julia; Nilsson, Juliet Fernanda; Niehaus, Karsten; Schlüter, Andreas; Pühler, Alfred; Del Papa, María Florencia; Lagares, Antonio; Martínez-Romero, Esperanza; Pistorio, Mariano

    2016-11-01

    Strains LPU83T and Or191 of the genus Rhizobium were isolated from the root nodules of alfalfa, grown in acid soils from Argentina and the USA. These two strains, which shared the same plasmid pattern, lipopolysaccharide profile, insertion-sequence fingerprint, 16S rRNA gene sequence and PCR-fingerprinting pattern, were different from reference strains representing species of the genus Rhizobium with validly published names. On the basis of previously reported data and from new DNA-DNA hybridization results, phenotypic characterization and phylogenetic analyses, strains LPU83T and Or191 can be considered to be representatives of a novel species of the genus Rhizobium, for which the name Rhizobium favelukesii sp. nov. is proposed. The type strain of this species is LPU83T (=CECT 9014T=LMG 29160T), for which an improved draft-genome sequence is available.

  2. 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.

  3. Complete Genome Sequences of Three Rhizobium gallicum Symbionts Associated with Common Bean (Phaseolus vulgaris)

    PubMed Central

    Bustos, Patricia; Santamaría, Rosa Isela; Pérez-Carrascal, Olga María; Acosta, José Luis; Lozano, Luis; Juárez, Soledad; Martínez-Romero, Esperanza; Cevallos, Miguel Ángel; Romero, David; Dávila, Guillermo; Vinuesa, Pablo; Miranda, Fabiola; Ormeño, Ernesto

    2017-01-01

    ABSTRACT The whole-genome sequences of three strains of Rhizobium gallicum reported here support the concept that the distinct nodulation host ranges displayed by the symbiovars gallicum and phaseoli can be largely explained by different symbiotic plasmids. PMID:28302777

  4. Genome sequence of the acid-tolerant strain Rhizobium sp. LPU83.

    PubMed

    Wibberg, Daniel; Tejerizo, Gonzalo Torres; Del Papa, María Florencia; Martini, Carla; Pühler, Alfred; Lagares, Antonio; Schlüter, Andreas; Pistorio, Mariano

    2014-04-20

    Rhizobia are important members of the soil microbiome since they enter into nitrogen-fixing symbiosis with different legume host plants. Rhizobium sp. LPU83 is an acid-tolerant Rhizobium strain featuring a broad-host-range. However, it is ineffective in nitrogen fixation. Here, the improved draft genome sequence of this strain is reported. Genome sequence information provides the basis for analysis of its acid tolerance, symbiotic properties and taxonomic classification.

  5. Permanent draft genome of the malachite-green-tolerant bacterium Rhizobium sp. MGL06.

    PubMed

    Liu, Yang; Wang, Runping; Zeng, Runying

    2014-12-01

    Rhizobium sp. MGL06, the first Rhizobium isolate from a marine environment, is a malachite-green-tolerant bacterium with a broader salinity tolerance (range: 0.5% to 9%) than other rhizobia. This study sequences and annotates the draft genome sequence of this strain. Genome sequence information provides a basis for analyzing the malachite green tolerance, broad salinity adaptation, nitrogen fixation properties, and taxonomic classification of the isolate.

  6. Introduction of a novel pathway for IAA biosynthesis to rhizobia alters vetch root nodule development.

    PubMed

    Camerini, Serena; Senatore, Beatrice; Lonardo, Enza; Imperlini, Esther; Bianco, Carmen; Moschetti, Giancarlo; Rotino, Giuseppe L; Campion, Bruno; Defez, Roberto

    2008-07-01

    We introduced into Rhizobium leguminosarum bv. viciae LPR1105 a new pathway for the biosynthesis of the auxin, indole-3-acetic acid (IAA), under the control of a stationary phase-activated promoter active both in free-living bacteria and bacteroids. The newly introduced genes are the iaaM gene from Pseudomonas savastanoi and the tms2 gene from Agrobacterium tumefaciens. Free-living bacteria harbouring the promoter-iaaMtms2 construct release into the growth medium 14-fold more IAA than the wild-type parental strain. This IAA overproducing R. l. viciae, the RD20 strain, elicits the development of vetch root nodules containing up to 60-fold more IAA than nodules infected by the wild-type strain LPR1105. Vetch root nodules derived from RD20 are fewer in number per plant, heavier in terms of dry weight and show an enlarged and more active meristem. A significant increase in acetylene reduction activity was measured in nodules elicited in vetch by RD20.

  7. Rhizobium helanshanense sp. nov., a bacterium that nodulates Sphaerophysa salsula (Pall.) DC. in China.

    PubMed

    Qin, Wei; Deng, Zhen Shan; Xu, Lin; Wang, Na Na; Wei, Ge Hong

    2012-05-01

    Studying rhizobia in the root nodules of Sphaerophysa salsula (Pall.) DC in the northwest of China, we obtained five strains classified as genus Rhizobium on the basis of their 16S rRNA gene sequences. The sequence similarity of strain CCNWQTX14(T) with the most related species was 99.0%. Further phylogenetic analysis of housekeeping genes (recA and atpD) suggested the five strains comprised a novel lineage within Rhizobium. The nifH and nodD gene sequences of CCNWQTX14(T) were phylogenetically closely related with those of Sinorhizobium kummerowiae and R. sphaerophysae, respectively. The five strains isolated from different places were also distinct from related Rhizobium species using ERIC fingerprint profiles. The DNA-DNA hybridization value was 41.8% between CCNWQTX14(T) and Rhizobium sphaerophysae CCNWGS0238(T). Our novel strains were only able to form effective nodules on its original host Sphaerophysa salsula. Our data showed that the five Rhizobium strains formed a unique genomic species, for which a novel species Rhizobium helanshanense sp. nov. is proposed. The type strain is CCNWQTX14(T) (=ACCC 16237(T) =HAMBI 3083(T)).

  8. 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.

  9. Rhizobium tubonense sp. nov., isolated from root nodules of Oxytropis glabra.

    PubMed

    Zhang, Rong Juan; Hou, Bao Chao; Wang, En Tao; Li, Ying; Zhang, Xiao Xia; Chen, Wen Xin

    2011-03-01

    Four rhizobial strains, designated CCBAU 85046(T), CCBAU 85051, CCBAU 85048 and CCBAU 85049, isolated from root nodules of Oxytropis glabra grown in Tibet, China, were previously defined, using amplified 16S rRNA gene restriction analysis, as a novel group within the genus Rhizobium. To clarify their taxonomic position, these strains were further analysed and compared with reference strains of related bacteria using a polyphasic approach. The 16S rRNA gene analysis showed that the four isolates formed a distinct phylogenetic lineage in the genus Rhizobium. The isolates showed highest sequence similarity (97.8  %) to Rhizobium indigoferae CCBAU 71042(T). Phenotypic and physiological tests, DNA-DNA hybridization, phylogenetic analyses of housekeeping genes recA, atpD and glnII and fatty acid profiles also indicated that these four strains constitute a novel group distinct from recognized species of the genus Rhizobium. Based on this evidence, strains CCBAU 85046(T), CCBAU 85051, CCBAU 85048 and CCBAU 85049 represent a novel species in the genus Rhizobium, for which the name Rhizobium tubonense sp. nov. is proposed. The type strain is CCBAU 85046(T) (=LMG 25225(T) =HAMBI 3066(T)) and its DNA G+C content is 59.52 % (T(m)). Strain CCBAU 85046(T) could form effective nodules on plant species Vigna unguiculata and Medicago sativa but not on its host of origin Oxytropis glabra.

  10. Rhizobium vignae sp. nov., a symbiotic bacterium isolated from multiple legume species.

    PubMed

    Ren, Da Wei; Chen, Wen Feng; Sui, Xin Hua; Wang, En Tao; Chen, Wen Xin

    2011-03-01

    A group of rhizobial strains isolated from nodules of multiple legume species grown in different geographical regions of China had identical 16S rRNA genes. Phylogenetic analysis based on the 16S rRNA gene sequences showed that the novel strains formed a subclade in the genus Rhizobium together with Rhizobium galegae, Rhizobium huautlense and Rhizobium alkalisoli, with 99.8  % gene sequence similarity between the strains. The DNA-DNA relatedness values between the representative strain CCBAU 05176(T) and R. galegae ATCC 43677(T), R. huautlense S02(T) and R. alkalisoli CCBAU 01393(T) were 22.6  %, 8.9  % and 15.9  %, respectively. The novel strains were distinguished from recognized species of the genus Rhizobium by using a polyphasic approach, including PCR-based restriction fragment length polymorphism analysis (RFLP) of the 16S-23S intergenic spacer (IGS), phenotypic and physiological tests, sequence comparisons of housekeeping genes and cellular fatty acid profiles. Therefore, it is suggested that this group of strains represents a novel species for which the name Rhizobium vignae sp. nov. is proposed. The type strain is CCBAU 05176(T) (=HAMBI 3039(T)=LMG 25447(T)).

  11. Rhizobium vallis sp. nov., isolated from nodules of three leguminous species.

    PubMed

    Wang, Fang; Wang, En Tao; Wu, Li Juan; Sui, Xin Hua; Li, Ying; Chen, Wen Xin

    2011-11-01

    Four bacterial strains isolated from root nodules of Phaseolus vulgaris, Mimosa pudica and Indigofera spicata plants grown in the Yunnan province of China were identified as a lineage within the genus Rhizobium according to the analysis of 16S rRNA gene sequences, sharing most similarity with Rhizobium lusitanum P1-7(T) (99.1 % sequence similarity) and Rhizobium rhizogenes IAM 13570(T) (99.0 %). These strains also formed a distinctive group from the reference strains for defined species of the genus Rhizobium in a polyphasic approach, including the phylogenetic analyses of the 16S rRNA gene and housekeeping genes (recA, atpD, glnII), DNA-DNA hybridization, BOX-PCR fingerprinting, phenotypic characterization, SDS-PAGE of whole-cell proteins, and cellular fatty acid profiles. All the data obtained in this study suggested that these strains represent a novel species of the genus Rhizobium, for which the name Rhizobium vallis sp. nov. is proposed. The DNA G+C content (mol%) of this species varied between 60.9 and 61.2 (T(m)). The type strain of R. vallis sp. nov. is CCBAU 65647(T) ( = LMG 25295(T) =HAMBI 3073(T)), which has a DNA G+C content of 60.9 mol% and forms effective nodules on Phaseolus vulgaris.

  12. A study in vitro of the sensitivity to antibiotics of Bacteroides fragilis.

    PubMed

    Ingham, H R; Selkon, J B; Codd, A A; Hale, J H

    1968-07-01

    During a two-year period of observation Bacteroides species were isolated from specimens of pus and vaginal swabs from 115 patients in this hospital. Thirty-five representative strains proved on examination to be Bacteroides fragilis. Minimal inhibitory and minimal bactericidal concentrations of six antibiotics for these strains were determined. All strains were resistant to streptomycin, neomycin, and polymyxin, slightly sensitive to penicillin and ampicillin, and fully sensitive to tetracycline, chloramphenicol, erythromycin, and lincomycin. The minimum bactericidal concentrations of chloramphenicol, erythromycin, and lincomycin were two to four times the minimal inhibitory concentrations. Tetracycline failed to exert any consistent bactericidal effect.The treatment of patients with infections caused by B. fragilis is discussed in the light of the findings in vitro.

  13. Molecular cloning and sequencing of the gene encoding the fimbrial subunit protein of Bacteroides gingivalis.

    PubMed Central

    Dickinson, D P; Kubiniec, M A; Yoshimura, F; Genco, R J

    1988-01-01

    The gene encoding the fimbrial subunit protein of Bacteroides gingivalis 381, fimbrilin, has been cloned and sequenced. The gene was present as a single copy on the bacterial chromosome, and the codon usage in the gene conformed closely to that expected for an abundant protein. The predicted size of the mature protein was 35,924 daltons, and the secretory form may have had a 10-amino-acid, hydrophilic leader sequence similar to the leader sequences of the MePhe fimbriae family. The protein sequence had no marked similarity to known fimbrial sequences, and no homologous sequences could be found in other black-pigmented Bacteroides species, suggesting that fimbrillin represents a class of fimbrial subunit protein of limited distribution. Images PMID:2895100

  14. 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.

  15. 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.

  16. Induction of host defences by Rhizobium during ineffective nodulation of pea (Pisum sativum L.) carrying symbiotically defective mutations sym40 (PsEFD), sym33 (PsIPD3/PsCYCLOPS) and sym42.

    PubMed

    Ivanova, Kira A; Tsyganova, Anna V; Brewin, Nicholas J; Tikhonovich, Igor A; Tsyganov, Viktor E

    2015-11-01

    Rhizobia are able to establish a beneficial interaction with legumes by forming a new organ, called the symbiotic root nodule, which is a unique ecological niche for rhizobial nitrogen fixation. Rhizobial infection has many similarities with pathogenic infection and induction of defence responses accompanies both interactions, but defence responses are induced to a lesser extent during rhizobial infection. However, strong defence responses may result from incompatible interactions between legumes and rhizobia due to a mutation in either macro- or microsymbiont. The aim of this research was to analyse different plant defence reactions in response to Rhizobium infection for several pea (Pisum sativum) mutants that result in ineffective symbiosis. Pea mutants were examined by histochemical and immunocytochemical analyses, light, fluorescence and transmission electron microscopy and quantitative real-time PCR gene expression analysis. It was observed that mutations in pea symbiotic genes sym33 (PsIPD3/PsCYCLOPS encoding a transcriptional factor) and sym40 (PsEFD encoding a putative negative regulator of the cytokinin response) led to suberin depositions in ineffective nodules, and in the sym42 there were callose depositions in infection thread (IT) and host cell walls. The increase in deposition of unesterified pectin in IT walls was observed for mutants in the sym33 and sym42; for mutant in the sym42, unesterified pectin was also found around degrading bacteroids. In mutants in the genes sym33 and sym40, an increase in the expression level of a gene encoding peroxidase was observed. In the genes sym40 and sym42, an increase in the expression levels of genes encoding a marker of hypersensitive reaction and PR10 protein was demonstrated. Thus, a range of plant defence responses like suberisation, callose and unesterified pectin deposition as well as activation of defence genes can be triggered by different pea single mutations that cause perception of an otherwise

  17. Bacteroides Fragilis OmpA: Utility as a Live Vaccine Vector for Biodefense Agents

    DTIC Science & Technology

    2008-01-01

    control number. PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ADDRESS. 1. REPORT DATE 29-01-2008 2. REPORT TYPE Annual 3. DATES COVERED 30 DEC 2006...Microbiology Letters (the original manuscript was returned with some revisions requested and has been resubmitted.) The submitted manuscript is attached...cardiac myxoma [4]. Bacteroides fragilis, a non-spore-forming, Gram-negative rod, is the most common anaerobic organism isolated from clinical

  18. Prevalence of Enterotoxigenic Bacteroides fragilis in Children with Diarrhea in Japan

    PubMed Central

    Kato, Naoki; Liu, Chengxu; Kato, Haru; Watanabe, Kunitomo; Nakamura, Haruhi; Iwai, Naoichi; Ueno, Kazue

    1999-01-01

    In age-matched controlled studies performed in Japan, enterotoxigenic Bacteroides fragilis was isolated from 14.9% of 114 children aged 1 to 14 years with antibiotic-unassociated diarrhea (AUD) and 6.5% of 108 children aged 1 to 6 years with antibiotic-associated diarrhea (AAD). The difference in comparison with control children, was significant for AUD children but not AAD children. PMID:9986859

  19. Bacteroides Fragilis OmpA: Utility as a Live Vaccine Vector for Biodefense Agents

    DTIC Science & Technology

    2009-01-01

    same results as the porin alone (data not shown). The supernatants containing the OmpA proteins were subjected to sodium dodecyl sulfate polyacrylamide ...thetaiotaomicron outer membrane protein that is essential for utilization of maltooligosaccharides and starch . J Bacteriol 178, 823-830. Reeves, A. R., Wang, G. R...Salyers, A. A. (1997).Characterization of four outer membrane proteins that play a role in utilization of starch by Bacteroides thetaiotaomicron

  20. Transport and catabolism of D-mannose in Rhizobium meliloti.

    PubMed Central

    Arias, A; Gardiol, A; Martínez-Drets, G

    1982-01-01

    Rhizobium meliloti L5-30 grows on D-mannose as the sole carbon source. The catabolic pathway of D-mannose was characterized. The following activities were present: mannose transport system, mannokinase, and mannosephosphate isomerase. Several mannose-negative mutants were selected; they were classified into three functional groups: group I, mannokinase and mannosephosphate isomerase defective: group II, mannokinase defective; and group III, mannosephosphate isomerase defective. Mannose uptake was an active process, since it was inhibited by azide, dinitrophenol, and cyanide, but not by fluoride or arsenate. Growth on succinate repressed mannose uptake activity. The mannose transport system was present in all the mutants. Uptake studies showed that mannose-negative mutants did not metabolize this sugar. PMID:6286588

  1. Symbiotic implications of type III protein secretion machinery in Rhizobium.

    PubMed

    Viprey, V; Del Greco, A; Golinowski, W; Broughton, W J; Perret, X

    1998-06-01

    The symbiotic plasmid of Rhizobium sp. NGR234 carries a cluster of genes that encodes components of a bacterial type III secretion system (TTSS). In both animal and plant pathogens, the TTSS is an essential component of pathogenicity. Here, we show that secretion of at least two proteins (y4xL and NolX) is controlled by the TTSS of NGR234 and occurs after the induction with flavonoids. Polar mutations in two TTSS genes, rhcN and the nod-box controlled regulator of transcription y4xl, block the secretion of both proteins and strongly affect the ability of NGR234 to nodulate a variety of tropical legumes including Pachyrhizus tuberosus and Tephrosia vogelii.

  2. Pigment production by Bacteroides species with reference to sub-classification.

    PubMed

    Duerden, B I

    1975-02-01

    All six reference strains of Bacteroides species, 36 laboratory isolates conforming to this group, and individual strains of Escherichia coli, Proteus mirabilis, Salmonella typhimurium and Clostridum welchii produced a dense black pigment, identified as ferrus sulphide, when grown in cooked-meat media containing cystine and ferrous sulphate. This was an indicator effect resulting from the production of H2S by the bacteria in the presence of ferrous ions and was unrelated to the characteristic pigment produced by strains of B. melaninogenicus when grown on blood agar. A pigment was extracted by ultrasonic disintegration of washed cells of three reference strains of B. melanino-genicus grown for 1 week in horse-blood broth and on human-blood agar. It was intracellular or cell-associated, soluble in water and had the spectrophotometric characteristics of a derivative of haemoglobin. No such pigment was extracted from strains of B. fragilis or B. necrophorus by similar procedures. Pigment production is a stable characteristic of those strains of Bacteroides called B. melaninogenicus and it is a significant property in the classification of the Bacteroides group. However, the pigment-producing strains are not a homogenous species, and there were considerable differences between the results of biochemical tests and antibograms obtained with the three strains of B. melaninogenicus.

  3. Natural occurrence of black-pigmented Bacteroides species in the gingival crevice of the squirrel monkey.

    PubMed Central

    Clark, W B; Magnusson, I; Abee, C; Collins, B; Beem, J E; McArthur, W P

    1988-01-01

    The objective of this study was to determine whether the squirrel monkey (Saimiri scuireus) is indigenously colonized with black-pigmented bacteroides (BPB) resembling human Bacteroides gingivalis and Bacteroides intermedius (suspected periodontal pathogens) and to determine the usefulness of the squirrel monkey as an in vivo model for studying colonization by putative pathogens. We assayed the subgingival plaques of 138 monkeys of various ages and in four different colonies for the presence of anaerobic BPB microorganisms. We also tested half the animals for the presence of Actinobacillus actinomycetemcomitans. Clinical indices and levels of serum antibody to B. gingivalis were recorded. We detected BPB in 50% of the animals and A. actinomycetemcomitans in 69% of the animals. The presence of BPB was generally associated with increased age, increased gingival index, presence of calculus, and increased levels of serum antibody. These data indicate that the squirrel monkey may be a good model for studying the parameters of natural infection of the gingival crevice with suspected periodontopathogenic BPB microorganisms. PMID:3410543

  4. Soybean (Glycine max. L.) and bacteroid glyoxylate cycle activities during nodular senescence.

    PubMed

    Fargeix, Christophe; Gindro, Katia; Widmer, François

    2004-02-01

    Soybean (Glycine max. L.) nodular senescence results in the dismantling of the peribacteroid membrane (PBM) and in an increase of soybean isocitrate lyase (ICL; EC 4.1.3.1) and malate synthase (MS; EC 4.1.3.2) mRNA and protein levels. This suggests that in senescing soybean nodular cells, the specific glyoxylate cycle enzyme activities might be induced to reallocate carbon obtained from the PBM degradation. In order to evaluate as well the carbon metabolism of the nitrogen-fixing Bradyrhizobium japonicum endosymbiotic bacteroids during nodular senescence, their glyoxylate cycle activities were also investigated. To this end, partial DNA sequences were isolated from their icl and ms genes, but the corresponding mRNAs were not detected in the microorganisms. It was also observed that the bacteroid ICL and MS activities were negligible during nodular senescence. This suggests that glyoxylate cycle activities are not reinitiated in the bacteroids under these physiological conditions. In case the microorganisms nevertheless feed on the PBM degradation products, this might occur via the citric acid cycle exclusively.

  5. A Bacteroides tetracycline resistance gene represents a new class of ribosome protection tetracycline resistance.

    PubMed Central

    Nikolich, M P; Shoemaker, N B; Salyers, A A

    1992-01-01

    The ribosome protection type of tetracycline resistance (Tcr) has been found in a variety of bacterial species, but the only two classes described previously, Tet(M) and Tet(O), shared a high degree of amino acid sequence identity (greater than 75%). Thus, it appeared that this type of resistance emerged recently in evolution and spread among different species of bacteria by horizontal transmission. We obtained the DNA sequence of a Tcr gene from Bacteroides, a genus of gram-negative, obligately anaerobic bacteria that is phylogenetically distant from the diverse species in which tet(M) and tet(O) have been found. The Bacteroides Tcr gene defines a new class of ribosome protection resistance genes, Tet(Q), and has a deduced amino acid sequence that was only 40% identical to Tet(M) or Tet(O). Like tet(M) and tet(O), tet(Q) appears to have spread by horizontal transmission, but only within the Bacteroides group. Images PMID:1339256

  6. 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

  7. 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

  8. Host Plant Cultivar Effects on Hydrogen Evolution by Rhizobium leguminosarum.

    PubMed

    Bedmar, E J; Edie, S A; Phillips, D A

    1983-08-01

    The effect of host plant cultivar on H(2) evolution by root nodules was examined in symbioses between Pisum sativum L. and selected strains of Rhizobium leguminosarum. Hydrogen evolution from root nodules containing Rhizobium represents the sum of H(2) produced by the nitrogenase enzyme complex and H(2) oxidized by any uptake hydrogenase present in those bacterial cells. Relative efficiency (RE) calculated as RE = 1 - (H(2) evolved in air/C(2) H(2) reduced) did not vary significantly among ;Feltham First,' ;Alaska,' and ;JI1205' peas inoculated with R. leguminosarum strain 300, which lacks uptake hydrogenase activity (Hup(-)). That observation suggests that the three host cultivars had no effect on H(2) production by nitrogenase. However, RE of strain 128C53 was significantly (P

  9. A rhamnose-deficient lipopolysaccharide mutant of Rhizobium sp. IRBG74 is defective in root colonization and beneficial interactions with its flooding-tolerant hosts Sesbania cannabina and wetland rice.

    PubMed

    Mitra, Shubhajit; Mukherjee, Arijit; Wiley-Kalil, Audrey; Das, Seema; Owen, Heather; Reddy, Pallavolu M; Ané, Jean-Michel; James, Euan K; Gyaneshwar, Prasad

    2016-10-01

    Rhizobium sp. IRBG74 develops a classical nitrogen-fixing symbiosis with the aquatic legume Sesbania cannabina (Retz.). It also promotes the growth of wetland rice (Oryza sativa L.), but little is known about the rhizobial determinants important for these interactions. In this study, we analyzed the colonization of S. cannabina and rice using a strain of Rhizobium sp. IRBG74 dually marked with β-glucuronidase and the green fluorescent protein. This bacterium colonized S. cannabina by crack entry and through root hair infection under flooded and non-flooded conditions, respectively. Rhizobium sp. IRBG74 colonized the surfaces of wetland rice roots, but also entered them at the base of lateral roots. It became endophytically established within intercellular spaces in the rice cortex, and intracellularly within epidermal and hypodermal cells. A mutant of Rhizobium sp. IRBG74 altered in the synthesis of the rhamnose-containing O-antigen exhibited significant defects, not only in nodulation and symbiotic nitrogen fixation with S. cannabina, but also in rice colonization and plant growth promotion. Supplementation with purified lipopolysaccharides from the wild-type strain, but not from the mutant, restored the beneficial colonization of rice roots, but not fully effective nodulation of S. cannabina Commonalities and differences in the rhizobial colonization of the roots of wetland legume and rice hosts are discussed.

  10. Y4lO of Rhizobium sp. strain NGR234 is a symbiotic determinant required for symbiosome differentiation.

    PubMed

    Yang, Feng-Juan; Cheng, Li-Li; Zhang, Ling; Dai, Wei-Jun; Liu, Zhe; Yao, Nan; Xie, Zhi-Ping; Staehelin, Christian

    2009-02-01

    Type 3 (T3) effector proteins, secreted by nitrogen-fixing rhizobia with a bacterial T3 secretion system, affect the nodulation of certain host legumes. The open reading frame y4lO of Rhizobium sp. strain NGR234 encodes a protein with sequence similarities to T3 effectors from pathogenic bacteria (the YopJ effector family). Transcription studies showed that the promoter activity of y4lO depended on the transcriptional activator TtsI. Recombinant Y4lO protein expressed in Escherichia coli did not acetylate two representative mitogen-activated protein kinase kinases (human MKK6 and MKK1 from Medicago truncatula), indicating that YopJ-like proteins differ with respect to their substrate specificities. The y4lO gene was mutated in NGR234 (strain NGROmegay4lO) and in NGR Omega nopL, a mutant that does not produce the T3 effector NopL (strain NGR Omega nopLOmegay4lO). When used as inoculants, the symbiotic properties of the mutants differed. Tephrosia vogelii, Phaseolus vulgaris cv. Yudou No. 1, and Vigna unguiculata cv. Sui Qing Dou Jiao formed pink effective nodules with NGR234 and NGR Omega nopL Omega y4lO. Nodules induced by NGR Omega y4lO were first pink but rapidly turned greenish (ineffective nodules), indicating premature senescence. An ultrastructural analysis of the nodules induced by NGR Omega y4lO revealed abnormal formation of enlarged infection droplets in ineffective nodules, whereas symbiosomes harboring a single bacteroid were frequently observed in effective nodules induced by NGR234 or NGR Omega nopL Omega y4lO. It is concluded that Y4lO is a symbiotic determinant involved in the differentiation of symbiosomes. Y4lO mitigated senescence-inducing effects caused by the T3 effector NopL, suggesting synergistic effects for Y4lO and NopL in nitrogen-fixing nodules.

  11. 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

  12. Rhizobium halophytocola sp. nov., isolated from the root of a coastal dune plant.

    PubMed

    Bibi, Fehmida; Chung, Eu Jin; Khan, Ajmal; Jeon, Che Ok; Chung, Young Ryun

    2012-08-01

    During a study of endophytic bacteria from coastal dune plants, a bacterial strain, designated YC6881(T), was isolated from the root of Rosa rugosa collected from the coastal dune areas of Namhae Island, Korea. The bacterium was found to be Gram-staining-negative, motile, halophilic and heterotrophic with a single polar flagellum. Strain YC6881(T) grew at temperatures of 4-37 °C (optimum, 28-32 °C), at pH 6.0-9.0 (optimum, pH 7.0-8.0), and at NaCl concentrations in the range of 0-7.5% (w/v) (optimum, 4-5% NaCl). Strain YC6881(T) was catalase- and oxidase-positive and negative for nitrate reduction. According to phylogenetic analysis using 16S rRNA gene sequences, strain YC6881(T) belonged to the genus Rhizobium and showed the highest 16S rRNA gene sequence similarity of 96.9% to Rhizobium rosettiformans, followed by Rhizobium borbori (96.3%), Rhizobium radiobacter (96.1%), Rhizobium daejeonense (95.9%), Rhizobium larrymoorei (95.6%) and Rhizobium giardinii (95.4%). Phylogenetic analysis of strain YC6881(T) by recA, atpD, glnII and 16S-23S intergenic spacer (IGS) sequences all confirmed the phylogenetic arrangements obtained by using 16S rRNA gene sequences. Cross-nodulation tests showed that strain YC6881(T) was a symbiotic bacterium that nodulated Vigna unguiculata and Pisum sativum. The major components of the cellular fatty acids were C(18:1)ω7c (53.7%), C(19:0) cyclo ω8c (12.6%) and C(12:0) (8.1%). The DNA G+C content was 52.8 mol%. Phenotypic and physiological tests with respect to carbon source utilization, antibiotic resistance, growth conditions, phylogenetic analyses of housekeeping genes recA, atpD and glnII, and fatty acid composition could be used to discriminate strain YC6881(T) from other species of the genus Rhizobium in the same sublineage. Based on the results obtained in this study, strain YC6881(T) is considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium halophytocola sp. nov. is proposed. The type

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

    PubMed

    Maróti, Gergely; Kondorosi, Eva

    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.

  14. 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

  15. 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.

  16. Only one catalase, katG, is detectable in Rhizobium etli, and is encoded along with the regulator OxyR on a plasmid replicon.

    PubMed

    Vargas, María del Carmen; Encarnación, Sergio; Dávalos, Araceli; Reyes-Pérez, Agustín; Mora, Yolanda; García-de los Santos, Alejandro; Brom, Susana; Mora, Jaime

    2003-05-01

    The plasmid-borne Rhizobium etli katG gene encodes a dual-function catalase-peroxidase (KatG) (EC 1.11.1.7) that is inducible and heat-labile. In contrast to other rhizobia, katG was shown to be solely responsible for catalase and peroxidase activity in R. etli. An R. etli mutant that did not express catalase activity exhibited increased sensitivity to hydrogen peroxide (H(2)O(2)). Pre-exposure to a sublethal concentration of H(2)O(2) allowed R. etli to adapt and survive subsequent exposure to higher concentrations of H(2)O(2). Based on a multiple sequence alignment with other catalase-peroxidases, it was found that the catalytic domains of the R. etli KatG protein had three large insertions, two of which were typical of KatG proteins. Like the katG gene of Escherichia coli, the R. etli katG gene was induced by H(2)O(2) and was important in sustaining the exponential growth rate. In R. etli, KatG catalase-peroxidase activity is induced eightfold in minimal medium during stationary phase. It was shown that KatG catalase-peroxidase is not essential for nodulation and nitrogen fixation in symbiosis with Phaseolus vulgaris, although bacteroid proteome analysis indicated an alternative compensatory mechanism for the oxidative protection of R. etli in symbiosis. Next to, and divergently transcribed from the catalase promoter, an ORF encoding the regulator OxyR was found; this is the first plasmid-encoded oxyR gene described so far. Additionally, the katG promoter region contained sequence motifs characteristic of OxyR binding sites, suggesting a possible regulatory mechanism for katG expression.

  17. 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

  18. Metronidazole in prevention and treatment of bacteroides infections after appendicectomy.

    PubMed Central

    Willis, A T; Ferguson, I R; Jones, P H; Phillips, K D; Tearle, P V; Berry, R B; Fiddian, R V; Graham, D F; Harland, D H; Innes, D B; Mee, W M; Rothwell-Jackson, R L; Sutch, I; Kilbey, C; Edwards, D

    1976-01-01

    The frequency of non-clostridial anaerobic infection was studied in 95 patients who had undergone acute appendicectomy: 49 received prophylactic metronidazole and 46 received placebo. Anaerobic infection did not develop in any of the metronidazole-treated patients, but infections did develop in nine (19%) of the 46 controls. Metronidazole is conveniently administered by suppository to patients who cannot take oral drugs. Five patients with intra-abdominal infections caused by non-clostridial anaerobes were successfully treated with metronidazole. PMID:764935

  19. 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)).

  20. Rhizobium tarimense sp. nov., isolated from soil in the ancient Khiyik River.

    PubMed

    Turdahon, Maripat; Osman, Ghenijan; Hamdun, Maryam; Yusuf, Khayir; Abdurehim, Zumret; Abaydulla, Gulsumay; Abdukerim, Muhtar; Fang, Chengxiang; Rahman, Erkin

    2013-07-01

    A Gram-negative, non-motile, pale-yellow, rod-shaped bacterial strain, PL-41(T), was isolated from Populus euphratica forest soil at the ancient Khiyik River valley in Xinjiang Uyghur Autonomous Region, People's Republic of China. Strain PL-41(T) grew optimally at 30 °C and pH 7.0-8.0. The major quinone was Q-10. The predominant cellular fatty acids of strain PL-41(T) were summed feature 8 (comprising C18 : 1ω7c and C18 : 1ω6c), C16 : 0 and C19 : 0 cyclo ω8c. Polar lipids of strain PL-41(T) include two unidentified aminophospholipids (APL1, 2), two unidentified phospholipids (PL1, 2), phosphatidylcholine and three unidentified lipids (L1-3). Strain PL-41(T) showed 16S rRNA gene sequence similarity of 97.0-97.5 % to the type strains of recognized species of the genus Rhizobium. Phylogenetic analysis of strain PL-41(T) based on the sequences of housekeeping genes recA and atpD confirmed (similarities are less than 90 %) its position as a distinct species of the genus Rhizobium. The DNA G+C content was 57.8 mol%. DNA-DNA relatedness between strain PL-41(T) and the type strains of Rhizobium huautlense S02(T), Rhizobium alkalisoli CCBAU 01393(T), Rhizobium vignae CCBAU 05176(T) and Rhizobium loessense CCBAU 7190B(T) were 33.4, 22.6, 25.5 and 45.1 %, respectively, indicating that strain PL-41(T) was distinct from them genetically. Strain PL-41(T) also can be differentiated from these four phylogenetically related species of the genus Rhizobium by various phenotypic properties. On the basis of phenotypic properties, phylogenetic distinctiveness and genetic data, strain PL-41(T) is considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium tarimense sp. nov. is proposed. The type strain is PL-41(T) ( = CCTCC AB 2011011(T) = NRRL B-59556(T)).

  1. Novel Rhizobium lineages isolated from root nodules of the common bean (Phaseolus vulgaris L.) in Andean and Mesoamerican areas.

    PubMed

    Ribeiro, Renan Augusto; Ormeño-Orrillo, Ernesto; Dall'Agnol, Rebeca Fuzinatto; Graham, Peter H; Martinez-Romero, Esperanza; Hungria, Mariangela

    2013-09-01

    The taxonomic affiliations of nineteen root-nodule bacteria isolated from the common bean (Phaseolus vulgaris L.) in Mexico, Ecuador and Brazil were investigated by analyses of 16S rRNA and of four protein-coding housekeeping genes. One strain from Mexico could be assigned to Rhizobium etli and two from Brazil to Rhizobium leucaenae, whereas another from Mexico corresponded to a recently described bean-nodulating species-level lineage related to R. etli and Rhizobium phaseoli. Ten strains isolated in Ecuador and Mexico corresponded to three novel Rhizobium lineages that fall into the R. phaseoli/R. etli/Rhizobium leguminosarum clade. One of those lineages, with representatives isolated mostly from Ecuador, seems to be dominant in beans from that Andean region. Only one of the Mexican strains clustered within the Rhizobium tropici clade, but as an independent lineage. Interestingly, four strains were affiliated with species within the Rhizobium radiobacter clade. The existence of yet non-described native Rhizobium lineages in both the Andean and Mesoamerican areas is discussed in relation to common-bean diversity and environmental conditions.

  2. Mapping the genetic basis of symbiotic variation in legume-rhizobium interactions in Medicago truncatula.

    PubMed

    Gorton, Amanda J; Heath, Katy D; Pilet-Nayel, Marie-Laure; Baranger, Alain; Stinchcombe, John R

    2012-11-01

    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.

  3. 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)).

  4. 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

  5. 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.

  6. 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

  7. Transcriptional activation of virulence genes of Rhizobium etli.

    PubMed

    Wang, Luyao; Lacroix, Benoît; Guo, Jianhua; Citovsky, Vitaly

    2017-01-09

    Recently, Rhizobium etli has emerged, in addition to Agrobacterium spp., as a prokaryotic species that encodes a functional machinery for DNA transfer to plant cells. To understand this R. etli-mediated genetic transformation, it would be useful to define how its vir genes respond to the host plants. Here, we explored the transcriptional activation of the vir genes contained on the R. etli p42a plasmid. Using a reporter construct harboring lacZ under the control of the R. etli virE promoter, we showed that the signal phenolic molecule acetosyringone (AS) induced R. etli vir gene expression both in R. etli and in A. tumefaciens background. Furthermore, in both bacterial backgrounds, the p42a plasmid also promoted plant genetic transformation with a reporter T-DNA. Importantly, the R. etli vir genes were transcriptionally activated by AS in a bacterial species-specific fashion in regard to the VirA/VirG signal sensor system, and this activation was induced by signals from the natural host species of this bacterium, but not from non-host plants. Early kinetics of transcriptional activation of the major vir genes of R. etli also revealed several features distinct from those known for A. tumefaciens: the expression of the virG gene reached saturation relatively quickly, and virB2, which in R. etli is located outside of the virB operon, was expressed only at low levels and did not respond to AS. These differences in vir gene transcription may contribute to the lower efficiency of T-DNA transfer of R. etli p42a versus pTiC58 of A. tumefaciens IMPORTANCE: The region encoding homologs of Agrobacterium tumefaciens virulence genes in the Rhizobium etli CE3 p42a plasmid was the first endogenous virulence system encoded by a non-Agrobacterium species demonstrated to be functional in DNA transfer and stable integration into plant cell genome. In this study, we explore the transcriptional regulation and induction of virulence genes in R. etli and show similarities and differences

  8. Monoclonal antibodies specific for Bacteroides fragilis enterotoxins BFT1 and BFT2 and their use in immunoassays

    PubMed Central

    Kaplan, Paul M.

    2017-01-01

    We have developed 22 mouse IgG1 monoclonal antibodies (mAbs) against Bacteroides fragilis zinc metalloprotease toxins 1 and 2 (BFT1 and BFT2). Mice were immunized with recombinant BFT1 or BFT2 proteins with metalloprotease activity. Eight of the mAbs bind specifically to BFT1. One mAb, 2H6, binds specifically to BFT2. The remaining 13 mAbs bind to both BFT1 and BFT2. The eight BFT1-specific mAbs recognize at least five different epitopes on the toxin. Four of the BFT1-specific mAbs neutralized rBFT1 metalloprotease activity. Only one of these four mAbs, 1D9, neutralizes the cytotoxic effect of BFT1. Here, we describe the development of enzyme-linked immunosorbent assays (ELISAs) to detect BFT1 or BFT2 toxin in an isotype-specific manner. The sandwich ELISAs have a detection limit of 20 to 40 ng/ml when purified recombinant BFT protein is diluted into PBS. The sandwich ELISA can be used to distinguish and quantify levels of rBFT1 and rBFT2 in stool. This ELISA can be an important tool to investigate the association between BFT expression by enterotoxigenic B. fragilis and diseases such as diarrhea, inflammatory bowel disease and colorectal cancer. PMID:28257448

  9. An electron microscope survey of the surface structures and hydrophobicity of oral and non-oral species of the bacterial genus Bacteroides.

    PubMed

    Handley, P S; Tipler, L S

    1986-01-01

    Seventeen strains of Bacteroides representing 10 species were examined by negative staining; the majority were from the mouth but a few non-oral strains were included. Seven species had peritrichously-arranged, non-flagellar appendages which could be divided by morphology and ultrastructure into two subgroups, fibrils and fimbriae. Bacteroides asaccharolyticus strains B536 and B537 and Bacteroides gingivalis strains W50, W83, WPH15 and WPH35 had fimbriae with mean width of 4.4 nm and 0.5 to 6.0 microns long depending on the strain. The fimbrial length within each strain also varied. Fibrils were present on two fresh oral isolates of Bacteroides melaninogenicus, Bacteroides intermedius strains T588 and W09, Bacteroides corporis ATCC 33547, Bacteroides oralis ATCC 33269 and Bacteroides buccae ATCC 33574. Fibrils consistently clumped into bundles of variable thickness and formed a fringe around the cell periphery, ranging from 0.27 to 1.2 microns long depending on the strain. Fibril lengths of each strain were uniform. Fibrils had no measurable width and the clumps tapered towards the free ends. Bacteroides loeschii VPI 9085, Bacteroides pentosaceus strains NP333 and J1 and Bacteroides capillosus 29799 had no detectable surface appendages. Fimbriate strains had a layer outside the outer membrane, with a mean thickness of between 17.8 and 28.6 nm. Both fibrillar and fimbriate strains produced many small membranous vesicles budding from the outer membrane. There were two morphological forms of vesicles, ones with either fimbriae or fibrils (species-dependent) and ones with no attached appendages. Of eleven strains tested for cell-surface hydrophobicity by partitioning between hexadecane and buffer, all but one was non-hydrophobic.

  10. [Nitrogenase, hydrogenase and nitrate reductase activities, oxygen consumption, and ATP content in nodules formed by strains of Rhizobium leguminosarum 128C53 and 300 in symbiosis with pea plants].

    PubMed

    Bedmar, E J; Olivares, J

    1986-10-01

    The nitrogenase activity, nitrate reductase activity and oxygen uptake as well as the hydrogen incorporation and ATP content were examined in the root nodules and bacteroids, respectively, formed by Rhizobium leguminosarum strains 128C53 (hydrogenase positive) and 300 (hydrogenase negative) in symbiosis with Pisum sativum plants grown in the presence of 2 mM KNO3. The strain 128C53 showed the greatest values for all parameters analyzed, except for the nitrate reductase activity, which was higher for the strain 300. Similarly, nodule nitrate reductase activity in strain 300 was greater than that in strain 128C53 when plants grew in the absence of combined nitrogen. In general, the highest values were obtained when determinations were made after 7 hours of plant illumination. However, the hydrogenase activity of strain 128C53 and the nitrate reductase activities of both strains increased with the light period, reaching a maximum after 14 hours of illumination. These results suggest that the benefits derived from the superior symbiotic properties and from the presence of hydrogenase activity in strain 128C53 could be counteracted by the higher rates of the nodule nitrate reductase activity in strain 300.

  11. Spinal epidural abscess caused by bacteroides fragilis group after dilation and curettage for incomplete abortion.

    PubMed

    Ohyagi, Masaki; Ohkubo, Takuya; Taniyama, Takashi; Tomizawa, Shoji; Okawa, Atsushi; Yokota, Takanori; Mizusawa, Hidehiro

    2012-04-01

    Spinal epidural abscess (SEA) is a rare infection complicated in patients who have some risk factors such as injection-drug use, diabetes mellitus, and several illnesses. However, no case of SEA associated with abortion has been reported. Here we report a case of SEA in a 30-year-old woman after dilation and curettage for incomplete abortion. The diagnosis of SEA was done by MRI and pus was drained after the cervical discectomy. Bacteroides fragilis group was cultured from the aspirated pus sample. The patient responded to surgical drainage and antibiotics.

  12. Cloning of Bacteroides fragilis plasmid genes affecting metronidazole resistance and ultraviolet survival in Escherichia coli

    SciTech Connect

    Wehnert, G.U.; Abratt, V.R.; Goodman, H.J.; Woods, D.R. )

    1990-03-01

    Since reduced metronidazole causes DNA damage, resistance to metronidazole was used as a selection method for the cloning of Bacteroides fragilis genes affecting DNA repair mechanisms in Escherichia coli. Genes from B. fragilis Bf-2 were cloned on a recombinant plasmid pMT100 which made E. coli AB1157 and uvrA, B, and C mutant strains more resistant to metronidazole, but more sensitive to far uv irradiation under aerobic conditions. The loci affecting metronidazole resistance and uv sensitivity were linked and located on a 5-kb DNA fragment which originated from the small 6-kb cryptic plasmid pBFC1 present in B. fragilis Bf-2 cells.

  13. Mycotic Aneurysm Caused by Bacteroides fragilis in an Elderly Immunosuppressed Patient

    PubMed Central

    Fukuchi, Takahiko; Kawasaki, Sadao; Hayashi, Hiroki; Koreeda, Daisuke; Ashikawa, Takahiro

    2016-01-01

    An 82-year-old Japanese man, who presented with a fever and abdominal pain, was admitted to our hospital. According to enhanced computed tomography images, the probable diagnosis was abdominal aortic mycotic aneurysm. Eight sets of blood cultures obtained from the patient were negative. Despite administering treatment with vancomycin and ceftriaxone, the aneurysm progressively enlarged. He underwent open debridement surgery and in situ replacement because of an aneurysmal rupture. Bacteroides fragilis was isolated from the tissue culture of the aortic wall. Metronidazole was administered and discontinued without any infection relapse. When faced with similar cases, rare pathogens should thus be considered as possible causes of mycotic aneurysms. PMID:27904124

  14. Processing parameters matching effects upon Rhizobium tropici biopolymers' rheological properties.

    PubMed

    Pimenta, Flávia Duta; Lopes, Léa Maria de Almeida; de França, Francisca Pessôa

    2008-07-01

    The combined effects of the processing parameters upon rheological properties of biopolymers produced by Rhizobium tropici were studied as a function of the Ca(+2) ions' concentration variation, yeast extract concentration added to the medium, aeration, and agitation, maintaining the mannitol concentration in 10 g/L. The experiments were carried out using a fermenter with 20-L capacity as a reactor. All processing parameters were monitored online. The temperature [(30 +/- 1) degrees C] and pH values (7.0) were kept constant throughout the experimental time. As a statistical tool, a complete 2(3) factorial design with central point and response surface was used to investigate the interactions between relevant variables of the fermentation process: calcium carbonate concentration, yeast extract concentration, aeration, and agitation. The processing parameter setup for reaching the maximum response for rheological propriety production was obtained when applying mannitol concentration of 10.0 g/L, calcium carbonate concentration 1.0 g/L, yeast extract concentration 1.0 g/L, aeration 1.30 vvm, and agitation 800 rpm. The viscosimetric investigation of polysaccharide solutions exposed their shear-thinning behavior and polyelectrolytic feature.

  15. 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.

  16. 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.)

  17. 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

  18. alpha-Ketoglutarate dehydrogenase mutant of Rhizobium meliloti.

    PubMed Central

    Duncan, M J; Fraenkel, D G

    1979-01-01

    A mutant of Rhizobium meliloti selected as unable to grow on L-arabinose also failed to grow on acetate or pyruvate. It grew, but slower than the parental strain, on many other carbon sources. Assay showed it to lack alpha-ketoglutarate dehydrogenase (kgd) activity, and revertants of normal growth phenotype contained the activity again. Other enzymes of the tricarboxylic acid cycle and of the glyoxylate cycle were present in both mutant and parent strains. Enzymes of pyruvate metabolism were also assayed. L-Arabinose degradation in R. meliloti was found to differ from the known pathway in R. japonicum, since the former strain lacked 2-keto-o-deoxy-L-arabonate aldolase but contained alpha-ketoglutarate semialdehyde dehydrogenase; thus, it is likely that R. meliloti has the L-arabinose pathway leading to alpha-ketoglutarate rather than the one to glycolaldehyde and pyruvate. This finding accounts for the L-arabinose negativity of the mutant. Resting cells of the mutant were able to metabolize the three substrates which did not allow growth. PMID:762018

  19. 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.

  20. 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. PMID:27635209

  1. The RPG gene of Medicago truncatula controls Rhizobium-directed polar growth during infection.

    PubMed

    Arrighi, Jean-François; Godfroy, Olivier; de Billy, Françoise; Saurat, Olivier; Jauneau, Alain; Gough, Clare

    2008-07-15

    Rhizobia can infect roots of host legume plants and induce new organs called nodules, in which they fix atmospheric nitrogen. Infection generally starts with root hair curling, then proceeds inside newly formed, intracellular tubular structures called infection threads. A successful symbiotic interaction relies on infection threads advancing rapidly at their tips by polar growth through successive cell layers of the root toward developing nodule primordia. To identify a plant component that controls this tip growth process, we characterized a symbiotic mutant of Medicago truncatula, called rpg for rhizobium-directed polar growth. In this mutant, nitrogen-fixing nodules were rarely formed due to abnormally thick and slowly progressing infection threads. Root hair curling was also abnormal, indicating that the RPG gene fulfils an essential function in the process whereby rhizobia manage to dominate the process of induced tip growth for root hair infection. Map-based cloning of RPG revealed a member of a previously unknown plant-specific gene family encoding putative long coiled-coil proteins we have called RRPs (RPG-related proteins) and characterized by an "RRP domain" specific to this family. RPG expression was strongly associated with rhizobial infection, and the RPG protein showed a nuclear localization, indicating that this symbiotic gene constitutes an important component of symbiotic signaling.

  2. Stable Tagging of Rhizobium meliloti with the Firefly Luciferase Gene for Environmental Monitoring

    PubMed Central

    Cebolla, Angel; Ruiz-Berraquero, Francisco; Palomares, Antonio Jose

    1993-01-01

    A system for stable tagging of gram-negative bacteria with the firefly luciferase gene, luc, is described. A previously constructed fusion constitutively expressing luc from the λpR promoter was used. Stable integration into the bacterial genome was achieved by use of mini-Tn5 delivery vectors. The procedure developed was applied for tagging of representative gram-negative bacteria, such as Escherichia coli, Rhizobium meliloti, Pseudomonas putida, and Agrobacterium tumefaciens. The system permitted the detection of tagged R. meliloti in the presence of more than 105 CFU per plate without the use of any selective markers (such as antibiotic resistance genes). No significant differences in growth rates or soil survival were found between the marked strain and the wild-type strain. Studies of bioluminescent R. meliloti also revealed a good correlation between cell biomass and bioluminescence. The firefly luciferase tagging system is an easy, safe, and sensitive method for the detection and enumeration of bacteria in the environment. Images PMID:16349015

  3. Rhizobium azibense sp. nov., a nitrogen fixing bacterium isolated from root-nodules of Phaseolus vulgaris.

    PubMed

    Mnasri, Bacem; Liu, Tian Yan; Saidi, Sabrine; Chen, Wen Feng; Chen, Wen Xin; Zhang, Xiao Xia; Mhamdi, Ridha

    2014-05-01

    Three microbial strains isolated from common beans, 23C2T (Tunisia), Gr42 (Spain) and IE4868 (Mexico), which have been identified previously as representing a genomic group closely related to Rhizobium gallicum, are further studied here. Their 16S rRNA genes showed 98.5-99% similarity with Rhizobium loessense CCBAU 7190BT, R. gallicum R602spT, Rhizobium mongolense USDA 1844T and Rhizobium yanglingense CCBAU 71623T. Phylogenetic analysis based on recA, atpD, dnaK and thrC sequences showed that the novel strains were closely related and could be distinguished from the four type strains of the closely related species. Strains 23C2T, Gr42 and IE4868 could be also differentiated from their closest phylogenetic neighbours by their phenotypic and physiological properties and their fatty acid contents. All three strains harboured symbiotic genes specific to biovar gallicum. Levels of DNA-DNA relatedness between strain 23C2T and the type strains of R. loessense, R. mongolense, R. gallicum and R. yanglingense ranged from 58.1 to 61.5%. The DNA G+C content of the genomic DNA of strain 23C2T was 59.52%. On the basis of these data, strains 23C2T, Gr42 and IE4868 were considered to represent a novel species of the genus Rhizobium for which the name Rhizobium azibense is proposed. Strain 23C2T (=CCBAU 101087T=HAMBI3541T) was designated as the type strain.

  4. Rhizobium skierniewicense sp. nov., isolated from tumours on chrysanthemum and cherry plum.

    PubMed

    Puławska, Joanna; Willems, Anne; Sobiczewski, Piotr

    2012-04-01

    Three isolates of Gram-negative, rod-shaped, non-spore-forming bacteria were recovered from galls on chrysanthemum (Chrysanthemum L.; Ch11T, Ch12) and cherry plum (Prunus cerasifera var. divaricata; AL9.3). All three isolates were able to cause crown galls on various plant species. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the three isolates were probably identical (100% sequence similarity) and closely related to Rhizobium rubi (99.6 %), Rhizobium radiobacter (98.7 %) and Rhizobium larrymoorei (98.1 %). Similar analysis based on the housekeeping genes glnA, gyrB and rpoB also indicated that the novel isolates were identical and closely related to R. rubi. The major cellular fatty acids of strain Ch11T were C18:1ω7c (62.1 %), summed feature 2 (comprising C12:0 aldehyde, iso-C16:1 I and/or C14:0 3-OH; 10.8 %), summed feature 3 (comprising C16:1ω7c and/or iso-C15:0 2-OH; 7.7 %) and C10:0 3-OH (7.5 %). However, the DNA-DNA relatedness between Ch11T and R. rubi LMG 156T was only 48 % and, unlike phylogenetically related established Rhizobium species, the novel isolates were able to utilize β-hydroxybutyric acid but not L-fucose. Based on the phylogenetic and phenotypic evidence, the isolates are considered to represent a single novel species of the genus Rhizobium, for which the name Rhizobium skierniewicense sp. nov. is proposed; the type strain is Ch11T (=LMG 26191T=CFBP 7420T).

  5. Rhizobium nepotum sp. nov. isolated from tumors on different plant species.

    PubMed

    Puławska, Joanna; Willems, Anne; De Meyer, Sofie E; Süle, Sandor

    2012-06-01

    Five Gram-negative, rod-shaped, non-spore-forming bacteria were isolated from galls on different plant species in Hungary: strain 39/7(T) from Prunus cerasifera Myrobalan, strain 0 from grapevine var. Ezerjó, strain 7/1 from raspberry var. Findus and in Poland, strain C3.4.1 from Colt rootstock (Prunus avium × Prunus pseudocerasus) and strain CP17.2.2 from Prunus avium. Only one of these isolates, strain 0, is able to cause crown gall on different plant species. On the basis of 16S rRNA gene sequence similarity, the strains cluster together and belong to the genus Rhizobium and their closest relative is Rhizobium radiobacter (99.1%). Phylogenetic analysis of the novel strains using housekeeping genes atpD, glnA, gyrB, recA and rpoB revealed their distinct position separate from other known Rhizobium species and confirmed their relation to Rhizobium radiobacter. The major cellular fatty acids are 18:1 w7c, 16:0, 16:0 3OH, summed feature 2 (comprising 12:0 aldehyde, 16:1 iso I and/or 14:0 3OH) and summed feature 3 (comprising 16:1 w7c and/or 15 iso 2OH). DNA-DNA hybridization of strain 39/7(T) with the type strain of R. radiobacter LMG 140(T) revealed 45% DNA-DNA hybridization. Phenotypic and physiological properties differentiate the novel isolates from other closely related species. On the basis of the results obtained, the five isolates are considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium nepotum sp. nov. (type strain 39/7(T)=LMG 26435(T)=CFBP 7436(T)) is proposed.

  6. Rhizobium pusense sp. nov., isolated from the rhizosphere of chickpea (Cicer arietinum L.).

    PubMed

    Panday, Digvijay; Schumann, Peter; Das, Subrata K

    2011-11-01

    A novel bacterial strain, designated NRCPB10(T), was isolated from rhizosphere soil of chickpea (Cicer arietinum L.) in Pusa, New Delhi, India. The 16S rRNA gene sequence of strain NRCPB10(T) showed highest similarity (98.9 %) to that of Rhizobium radiobacter NCPPB 2437(T), followed by Rhizobium larrymoorei AF3-10(T) (97.7 %) and Rhizobium rubi IFO 13261(T) (97.4 %). Phylogenetic analysis of strain NRCPB10(T) based on the housekeeping genes recA and atpD confirmed its position as distinct from recognized Rhizobium species. Levels of DNA-DNA relatedness between strain NRCPB10(T) and R. radiobacter ICMP 5785(T), R. larrymoorei LMG 21410(T) and R. rubi ICMP 6428(T) were 51.0, 32.6 and 27.3 %, respectively. Cellular fatty acids of strain NRCPB10(T) were C(18 : 1)ω7c (58.9 %), C(16 : 0) (15.5 %), C(19 : 0) cyclo ω8c (11.5 %), iso-C(16 : 1) (5.8 %), C(16 : 0) 3-OH (4.5 %), C(16 : 1)ω7c (2.1 %) and C(18 : 0) (1.3 %). The G+C content of the genomic DNA of strain NRCPB10(T) was 59.0 mol%. Strain NRCPB10(T) did not nodulate chickpea plants or induce tumours in tobacco plants. Phenotypic and physiological properties along with SDS-PAGE of whole-cell soluble proteins differentiated strain NRCPB10(T) from its closest phylogenetic neighbours. On the basis of data from the present polyphasic taxonomic study, strain NRCPB10(T) is considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium pusense sp. nov. is proposed. The type strain is NRCPB10(T) ( = LMG 25623(T) = JCM 16209(T) = NCIMB 14639(T)).

  7. 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

  8. 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.

  9. 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.

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

    DOE PAGES

    Sakamoto, Mitsuo; Lapidus, Alla L.; Han, James; ...

    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.

  11. High quality draft genome sequence of Bacteroides barnesiae type strain BL2(T) (DSM 18169(T)) from chicken caecum.

    PubMed

    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

    2015-01-01

    Bacteroides barnesiae Lan et al. 2006 is a species of the genus Bacteroides, which belongs to the family Bacteroidaceae. Strain BL2(T) 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. 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.

  12. 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.

  13. 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

  14. Multiple Signals Govern Utilization of a Polysaccharide in the Gut Bacterium Bacteroides thetaiotaomicron

    PubMed Central

    Schwalm, Nathan D.; Townsend, Guy E.

    2016-01-01

    ABSTRACT The utilization of simple sugars is widespread across all domains of life. In contrast, the breakdown of complex carbohydrates is restricted to a subset of organisms. A regulatory paradigm for integration of complex polysaccharide breakdown with simple sugar utilization was established in the mammalian gut symbiont Bacteroides thetaiotaomicron, whereby sensing of monomeric fructose regulates catabolism of both fructose and polymeric fructans. We now report that a different regulatory paradigm governs utilization of monomeric arabinose and the arabinose polymer arabinan. We establish that (i) arabinan utilization genes are controlled by a transcriptional activator that responds to arabinan and by a transcriptional repressor that responds to arabinose, (ii) arabinose utilization genes are regulated directly by the arabinose-responding repressor but indirectly by the arabinan-responding activator, and (iii) activation of both arabinan and arabinose utilization genes requires a pleiotropic transcriptional regulator necessary for survival in the mammalian gut. Genomic analysis predicts that this paradigm is broadly applicable to the breakdown of other polysaccharides in both B. thetaiotaomicron and other gut Bacteroides spp. The uncovered mechanism enables regulation of polysaccharide utilization genes in response to both the polysaccharide and its breakdown products. PMID:27729509

  15. 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

  16. [Possible role of enterotoxigenic Bacteroides fragilis in the etiology of infectious vaginitis].

    PubMed

    Polanco, Nina; Manzi, Lorna; Carmona, Oswaldo

    2012-03-01

    Vaginitis is a common gynecologic disorder. It is due to several causes, some even unknown. Bacteroides fragilis is the most important anaerobe in clinical bacteriology, some strains of this group are notable for being enterotoxigenic and they have been associated with intestinal and extraintestinal syndromes. They have recently been isolated from patients with vaginitis. The purpose of this study was to investigate a possible association of enterotoxigenic B. fragilis with infectious vaginitis. 265 samples of vaginal exudate were processed, 202 from symptomatic patients and 63 healthy women. The identification of the microorganisms was carried out by conventional methods. In 31.2% of symptomatic patients were identified: Gardnerella vaginalis, Mobiluncus, Candida albicans, Mycoplasma hominis, Ureaplasma urealyticum and Streptococcus agalactiae. B. fragilis was identified in 27 symptomatic patients and 5 healthy women. These strains were cultivated in liquid medium and incubated during 48 h at 36 degrees C in anaerobe chambers. Supernatant activity was assayed in HT-29 cells. Eighteen B. fragilis strains isolated from symptomatic patients were enterotoxigenic, because induced alterations in target cell morphology. It was not identified in healthy women (P < 0.05). 77.7% of enterotoxigenic B. fragilis strains were not associated with other specific pathogens. This fact suggests that enterotoxigenic B. fragilis could be a cause for vaginitis. The effect of enterotoxin on E-cadherin of vaginal epithelium could facilitate invasion and its possible pathogenic role in the vagina. This is the first report that associates enterotoxigenic Bacteroides fragilis as a possible cause of infectious vaginitis.

  17. Inactivation of a single gene enables microaerobic growth of the obligate anaerobe Bacteroides fragilis

    PubMed Central

    Meehan, Brian M.; Baughn, Anthony D.; Gallegos, Rene; Malamy, Michael H.

    2012-01-01

    Bacteroides fragilis can replicate in atmospheres containing ≤0.05% oxygen, but higher concentrations arrest growth by an unknown mechanism. Here we show that inactivation of a single gene, oxe (i.e., oxygen enabled) in B. fragilis allows for growth in concentrations as high as 2% oxygen while increasing the tolerance of this organism to room air. Known components of the oxidative stress response including the ahpC, kat, batA-E, and tpx genes were not individually important for microaerobic growth. However, a Δoxe strain scavenged H2O2 at a faster rate than WT, indicating that reactive oxygen species may play a critical role in limiting growth of this organism to low-oxygen environments. Clinical isolates of B. fragilis displayed a greater capacity for growth under microaerobic conditions than fecal isolates, with some encoding polymorphisms in oxe. Additionally, isolation of oxygen-enabled mutants of Bacteroides thetaiotaomicron suggests that Oxe may mediate growth arrest of other anaerobes in oxygenated environments. PMID:22778399

  18. Medicago truncatula root nodule proteome analysis reveals differential plant and bacteroid responses to drought stress.

    PubMed

    Larrainzar, Estíbaliz; Wienkoop, Stefanie; Weckwerth, Wolfram; Ladrera, Rubén; Arrese-Igor, Cesar; González, Esther M

    2007-07-01

    Drought is one of the environmental factors most affecting crop production. Under drought, symbiotic nitrogen fixation is one of the physiological processes to first show stress responses in nodulated legumes. This inhibition process involves a number of factors whose interactions are not yet understood. This work aims to further understand changes occurring in nodules under drought stress from a proteomic perspective. Drought was imposed on Medicago truncatula 'Jemalong A17' plants grown in symbiosis with Sinorhizobium meliloti strain 2011. Changes at the protein level were analyzed using a nongel approach based on liquid chromatography coupled to tandem mass spectrometry. Due to the complexity of nodule tissue, the separation of plant and bacteroid fractions in M. truncatula root nodules was first checked with the aim of minimizing cross contamination between the fractions. Second, the protein plant fraction of M. truncatula nodules was profiled, leading to the identification of 377 plant proteins, the largest description of the plant nodule proteome so far. Third, both symbiotic partners were independently analyzed for quantitative differences at the protein level during drought stress. Multivariate data mining allowed for the classification of proteins sets that were involved in drought stress responses. The isolation of the nodule plant and bacteroid protein fractions enabled the independent analysis of the response of both counterparts, gaining further understanding of how each symbiotic member is distinctly affected at the protein level under a water-deficit situation.

  19. Activation of Bacteroides fragilis toxin by a novel bacterial protease contributes to anaerobic sepsis

    PubMed Central

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

    2016-01-01

    Bacteroides fragilis is the leading cause of anaerobic bacteremia and sepsis 1. Enterotoxigenic strains producing B. fragilis toxin (BFT, fragilysin) contribute to colitis 2 and intestinal malignancy 3, yet are also isolated in bloodstream infection 4,5. 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 and identify a B. fragilis protease, fragipain (Fpn), which is required for endogenous activation of BFT through removal of its auto-inhibitory prodomain. Structural analysis of Fpn reveals a His-Cys catalytic dyad characteristic of C11 family cysteine proteases that are conserved in multiple pathogenic Bacteroides spp and Clostridium spp. Fpn-deficient enterotoxigenic B. fragilis is attenuated in its ability to induce sepsis, 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, indicating a greater complexity of cellular targeting and action of BFT than previously appreciated. The expression of fpn by both toxigenic and non-toxigenic strains suggests this protease may contribute to anaerobic sepsis beyond its role in toxin activation, potentially serving as a target for disease modification. PMID:27089515

  20. Sodium Stimulation of Uptake Hydrogenase Activity In Symbiotic Rhizobium1

    PubMed Central

    Kapulnik, Yoram; Phillips, Donald A.

    1986-01-01

    Initial observations showed a 100% increase in H2-uptake (Hup) activity of Rhizobium leguminosarum strain 3855 in pea root nodules (Pisum sativum L. cv Alaska) on plants growing in a baked clay substrate relative to those growing in vermiculite, and an investigation of nutrient factors responsible for the phenomenon was initiated. Significantly greater Hup activity was first measured in the clay-grown plants 24 days after germination, and higher activity was maintained relative to the vermiculite treatment until experiments were terminated at day 32. The increase in Hup activity was associated with a decrease in H2 evolution for plants with comparable rates of acetylene reduction. Analyses of the clay showed that it contained more Na+ (29 versus 9 milligrams per kilogram) and less K+ (6 versus 74 milligrams per kilogram) than the vermiculite. Analyses of plants, however, showed a large increase in Na+ concentration of clay-grown plants with a much smaller reduction in K+ concentration. In tests with the same organisms in a hydroponic system with controlled pH, 40 millimolar NaCl increased Hup activity more than 100% over plants grown in solutions lacking NaCl. Plants with increased Hup activity, however, did not have greater net carbon or total nitrogen assimilation. KCl treatments from 5 to 80 millimolar produced slight increased in Hup activity at 10 millimolar KCl, and tests with other salts in the hydroponic system indicated that only Na+ strongly promoted Hup activity. Treating vermiculite with 50 millimolar NaCl increased Na+ concentration in pea plant tissue and greatly promoted Hup activity of root nodules in a manner analogous to the original observation with the clay rooting medium. A wider generality of the phenomenon was suggested by demonstrating that exogenous Na+ increased Hup activity of other R. leguminosarum strains and promoted Hup activity of R. meliloti strain B300 in alfalfa (Medicago sativa L.). PMID:16665057

  1. Genetic regulation of nitrogen fixation in Rhizobium meliloti.

    PubMed

    Cebolla, A; Palomares, A J

    1994-12-01

    The soil bacterium Rhizobium meliloti fixes dinitrogen when associated with root nodules formed on its plant host, Medicago sativa (alfalfa). The expression of most of the known genes required for nitrogen fixation (nif and fix genes), including the structural genes for nitrogenase, is induced in response to a decrease in oxygen concentration. Induction of nif and fix gene expression by low oxygen is physiologically relevant because a low-oxygen environment is maintained in root nodules to prevent inactivation of the highly oxygen-sensitive nitrogenase enzyme. The genes responsible for sensing and transducing the low oxygen signal, fixL and fixJ, encode proteins (FixL and FixJ, respectively) that are homologous to a large family of bacterial proteins involved in signal transduction, the two component regulatory system proteins. The two components consist of a sensor protein, to which FixL is homologous, and a response regulator protein, to which FixJ is homologous. The sensor protein respond to an activating signal by autophosphorylating and then transferring the phosphate to its cognate response regulator protein. The phosphorylated response regulator, which is often a transcriptional activator, is then able to activate its target. A cascade model of nif and fix gene regulation in R. meliloti has been proposed, whereby FixL acts as an oxygen sensor as the initial event in the cascade and transmits this information to FixJ. FixJ, which possesses a putative helix-turn-helix DNA-binding motif, then activates transcription of the nifA and fixK genes. The nifA and fixK gene products, are transcriptional activators of at least 14 other nif and fix genes.

  2. Nitrogen fixation ability of exopolysaccharide synthesis mutants of Rhizobium sp. strain NGR234 and Rhizobium trifolii is restored by the addition of homologous exopolysaccharides.

    PubMed Central

    Djordjevic, S P; Chen, H; Batley, M; Redmond, J W; Rolfe, B G

    1987-01-01

    Several transposon Tn5-induced mutants of the broad-host-range Rhizobium sp. strain NGR234 produce little or no detectable acidic exopolysaccharide (EPS) and are unable to induce nitrogen-fixing nodules on Leucaena leucocephala var. Peru or siratro plants. The ability of these Exo- mutants to induce functioning nodules on Leucaena plants was restored by coinoculation with a Sym plasmid-cured (Nod- Exo+) derivative of parent strain NGR234, purified EPS from the parent strain, or the oligosaccharide from the EPS. Coinoculation with EPS or related oligosaccharide also resulted in formation of nitrogen-fixing nodules on siratro plants. In addition, an Exo- mutant (ANU437) of Rhizobium trifolii ANU794 was able to form nitrogen-fixing nodules on white clover in the presence of added EPS or related oligosaccharide from R. trifolii ANU843. These results demonstrate that the absence of Rhizobium EPSs can result in failure of effective symbiosis with both temperate and subtropical legumes. Images PMID:3025187

  3. 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...

  4. 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...

  5. Bioinformatic evidence and characterization of novel putative large conjugative transposons residing in genomes of genera Bacteroides and Prevotella.

    PubMed

    Gorenc, Katja; Accetto, Tomaž; Avguštin, Gorazd

    2012-07-01

    Bioinformatic evidence of the presence of a large conjugative transposon in ruminal bacterium Prevotella bryantii B(1)4(T) is presented. The described transposon appears to be related to another large conjugative transposon CTnBST, described in Bacteroides uniformis WH207 and to the conjugative transposon CTn3-Bf, which was observed in the genome of Bacteroides fragilis strain YCH46. All three transposons share tra gene regions with high amino acid identity and clearly conserved gene order. Additionally, a second conserved region consisting of hypothetical genes was discovered in all three transposons and named the GG region. This region served as a specific sequence signature and made possible the discovery of several other apparently related hypothetical conjugative transposons in bacteria from the genus Bacteroides. A cluster of genes involved in sugar utilization and metabolism was discovered within the hypothetical CTnB(1)4, to a certain extent resembling the polysaccharide utilization loci which were described recently in some Bacteroides strains. This is the first firm report on the presence of a large mobile genetic element in any strain from the genus Prevotella.

  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. 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...

  8. Rhizobium Lipo-chitooligosaccharide Signaling Triggers Accumulation of Cytokinins in Medicago truncatula Roots.

    PubMed

    van Zeijl, Arjan; Op den Camp, Rik H M; Deinum, Eva E; Charnikhova, Tatsiana; Franssen, Henk; Op den Camp, Huub J M; Bouwmeester, Harro; Kohlen, Wouter; Bisseling, Ton; Geurts, René

    2015-08-01

    Legume rhizobium symbiosis is initiated upon perception of bacterial secreted lipo-chitooligosaccharides (LCOs). Perception of these signals by the plant initiates a signaling cascade that leads to nodule formation. Several studies have implicated a function for cytokinin in this process. However, whether cytokinin accumulation and subsequent signaling are an integral part of rhizobium LCO signaling remains elusive. Here, we show that cytokinin signaling is required for the majority of transcriptional changes induced by rhizobium LCOs. In addition, we demonstrate that several cytokinins accumulate in the root susceptible zone 3 h after rhizobium LCO application, including the biologically most active cytokinins, trans-zeatin and isopentenyl adenine. These responses are dependent on calcium- and calmodulin-dependent protein kinase (CCaMK), a key protein in rhizobial LCO-induced signaling. Analysis of the ethylene-insensitive Mtein2/Mtsickle mutant showed that LCO-induced cytokinin accumulation is negatively regulated by ethylene. Together with transcriptional induction of ethylene biosynthesis genes, it suggests a feedback loop negatively regulating LCO signaling and subsequent cytokinin accumulation. We argue that cytokinin accumulation is a key step in the pathway leading to nodule organogenesis and that this is tightly controlled by feedback loops.

  9. Rhizobium freirei sp. nov., a symbiont of Phaseolus vulgaris that is very effective at fixing nitrogen.

    PubMed

    Dall'Agnol, Rebeca Fuzinatto; Ribeiro, Renan Augusto; Ormeño-Orrillo, Ernesto; Rogel, Marco Antonio; Delamuta, Jakeline Renata Marçon; Andrade, Diva Souza; Martínez-Romero, Esperanza; Hungria, Mariangela

    2013-11-01

    Common bean (Phaseolus vulgaris L.) can establish symbiotic associations with several Rhizobium species; however, the effectiveness of most strains at fixing nitrogen under field conditions is very low. PRF 81(T) is a very effective strain, usually referred to as Rhizobium tropici and used successfully in thousands of doses of commercial inoculants for the common bean crop in Brazil; it has shown high rates of nitrogen fixation in all areas representative of the crop in the country. Here, we present results that indicate that PRF 81(T), although it belongs to the 'R. tropici group', which includes 10 Rhizobium species, R. tropici, R. leucaenae, R. lusitanum, R. multihospitium, R. miluonense, R. hainanense, R. calliandrae, R. mayense, R. jaguaris and R. rhizogenes, represents a novel species. Several morpho-physiological traits differentiated PRF 81(T) from related species. Differences were also confirmed in the analysis of rep-PCR (sharing less than 45 % similarity with the other species), MLSA with recA, atpD and rpoB genes, and DNA-DNA hybridization. The novel species, for which we propose the name Rhizobium freirei sp. nov., is able to establish effective root nodule symbioses with Phaseolus vulgaris, Leucaena leucocephala, Leucaena esculenta, Crotalaria juncea and Macroptilium atropurpureum. The type strain is PRF 81(T) ( = CNPSo 122(T) = SEMIA 4080(T) = IPR-Pv81(T) = WDCM 440(T)).

  10. 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...

  11. Genome Sequence of the Symbiotic Type Strain Rhizobium tibeticum CCBAU85039T

    PubMed Central

    Wibberg, Daniel; Winkler, Anika; Ormeño-Orrillo, Ernesto; Martínez-Romero, Esperanza; Niehaus, Karsten; Pühler, Alfred; Kalinowski, Jörn; Lagares, Antonio; Schlüter, Andreas; Pistorio, Mariano

    2017-01-01

    ABSTRACT Rhizobium tibeticum was originally isolated from root nodules of Trigonella archiducis-nicolai grown in Tibet, China. This species is also able to nodulate Medicago sativa and Phaseolus vulgaris. The whole-genome sequence of the type strain, R. tibeticum CCBAU85039T, is reported in this study. PMID:28126941

  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).

  13. Draft Genome Sequence of Cupriavidus UYMMa02A, a Novel Beta-Rhizobium Species

    PubMed Central

    Iriarte, Andrés; Platero, Raúl; Romero, Valeria; Fabiano, Elena

    2016-01-01

    We present the draft genome of Cupriavidus UYMMa02A, a rhizobium strain isolated from root nodules of Mimosa magentea. The assembly has approximately 8.1 million bp with an average G+C of 64.1%. Symbiotic and metal-resistance genes were identified. The study of this genome will contribute to the understanding of rhizobial evolution. PMID:27834710

  14. 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. ...

  15. 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

  16. Genome Sequence of the Symbiotic Type Strain Rhizobium tibeticum CCBAU85039T.

    PubMed

    Torres Tejerizo, Gonzalo; Wibberg, Daniel; Winkler, Anika; Ormeño-Orrillo, Ernesto; Martínez-Romero, Esperanza; Niehaus, Karsten; Pühler, Alfred; Kalinowski, Jörn; Lagares, Antonio; Schlüter, Andreas; Pistorio, Mariano

    2017-01-26

    Rhizobium tibeticum was originally isolated from root nodules of Trigonella archiducis-nicolai grown in Tibet, China. This species is also able to nodulate Medicago sativa and Phaseolus vulgaris The whole-genome sequence of the type strain, R. tibeticum CCBAU85039(T), is reported in this study.

  17. 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.

  18. 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).

  19. Rhizobium populi sp. nov., an endophytic bacterium isolated from Populus euphratica.

    PubMed

    Rozahon, Manziram; Ismayil, Nurimangul; Hamood, Buayshem; Erkin, Raziya; Abdurahman, Mehfuzem; Mamtimin, Hormathan; Abdukerim, Muhtar; Lal, Rup; Rahman, Erkin

    2014-09-01

    An endophytic bacterium, designated K-38(T), was isolated from the storage liquid in the stems of Populus euphratica trees at the ancient Ugan River in Xinjiang, PR China. Strain K-38(T) was found to be rod-shaped, Gram-stain-negative, aerobic, non-motile and non-spore-forming. Strain K-38(T) grew at temperatures of 25-37 °C (optimum, 28 °C), at pH 6.0-9.0 (optimum, pH 7.5) and in the presence of 0-3 % (w/v) NaCl with 1 % as the optimum concentration for growth. According to phylogenetic analysis based on 16S rRNA gene sequences, strain K-38(T) was assigned to the genus Rhizobium with highest 16S rRNA gene sequence similarity of 97.2 % to Rhizobium rosettiformans W3(T), followed by Rhizobium nepotum 39/7(T) (96.5 %) and Rhizobium borbori DN316(T) (96.2 %). Phylogenetic analysis of strain K-38(T) based on the protein coding genes recA, atpD and nifH confirmed (similarities were less than 90 %) it to be a representative of a distinctly delineated species of the genus Rhizobium. The DNA G+C content was determined to be 63.5 mol%. DNA-DNA relatedness between K-38(T) and R. rosettiformans W3(T) was 48.4 %, indicating genetic separation of strain K-38(T) from the latter strain. The major components of the cellular fatty acids in strain K-38(T) were revealed to be summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c; 57.2 %), C16 : 0 (13.6 %) and summed feature 2 (comprising C12 : 0 aldehyde, C14 : 0 3-OH/iso-C16 : 1 I and/or unknown ECL 10.928; 11.0 %). Polar lipids of strain K-38(T) include phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, two unidentified aminophospholipids and two unidentified phospholipids. Q-10 was the major quinone in strain K-38(T). Based on phenotypic, chemotaxonomic and phylogenetic properties, strain K-38(T) represents a novel species of the genus Rhizobium, for which the name Rhizobium populi sp. nov. is proposed

  20. Application of a direct fluorescence-based live/dead staining combined with fluorescence in situ hybridization for assessment of survival rate of Bacteroides spp. in drinking water.

    PubMed

    Savichtcheva, Olga; Okayama, Noriko; Ito, Tsukasa; Okabe, Satoshi

    2005-11-05

    To evaluate the viability and survival ability of fecal Bacteroides spp. in environmental waters, a fluorescence-based live/dead staining method using ViaGram Red+ Bacterial gram stain and viability kit was combined with fluorescent in situ hybridization (FISH) with 16S rRNA-targeted oligonucleotide probe (referred as LDS-FISH). The proposed LDS-FISH was a direct and reliable method to detect fecal Bacteroides cells and their viability at single-cell level in complex microbial communities. The pure culture of Bacteroides fragilis and whole human feces were dispersed in aerobic drinking water and incubated at different water temperatures (4 degrees C, 13 degrees C, 18 degrees C, and 24 degrees C), and then the viability of B. fragilis and fecal Bacteroides spp. were determined by applying the LDS-FISH. The results revealed that temperature and the presence of oxygen have significant effects on the survival ability. Increasing the temperature resulted in a rapid decrease in the viability of both pure cultured B. fragilis cells and fecal Bacteroides spp. The live pure cultured B. fragilis cells could be found at the level of detection in drinking water for 48 h of incubation at 24 degrees C, whereas live fecal Bacteroides spp. could be detected for only 4 h of incubation at 24 degrees C. The proposed LDS-FISH method should provide useful quantitative information on the presence and viability of Bacteroides spp., a potential alternative fecal indicator, in environmental waters.

  1. Rhizobium smilacinae sp. nov., an endophytic bacterium isolated from the leaf of Smilacina japonica.

    PubMed

    Zhang, Lei; Shi, Xu; Si, Meiru; Li, Changfu; Zhu, Lingfang; Zhao, Liang; Shen, Xihui; Wang, Yao

    2014-10-01

    During a study of endophytic bacteria from traditional Chinese medicinal plants, a bacterial strain, designated PTYR-5(T), was isolated from the leaf of Smilacina japonica A. Gray collected from Taibai Mountain in Shaanxi Province, north-west China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PTYR-5(T) is a member of the genus Rhizobium, exhibiting the highest sequence similarities to R. cellulosilyticum LMG 23642(T) (97.2%), R. huautlense LMG 18254(T) (97.2%) and R. alkalisoli CCBAU 01393(T) (97.1%). The levels of 16S rRNA gene sequence similarity with respect to other Rhizobium species with validly published names were less than 97.0%. Phylogenies of the housekeeping genes atpD, recA and glnII confirmed its distinct position, showing low similarity with respect to those of recognized Rhizobium species (no more than 94.1, 90.0 and 88.0% similarity, respectively). The DNA-DNA relatedness values of strain PTYR-5(T) with R. cellulosilyticum LMG 23642(T), R. huautlense LMG 18254(T) and R. alkalisoli CCBAU 01393(T) were 33.6, 21.4 and 29.5 %, respectively. Based on phenotypic, phylogenetic and genotypic data, strain PTYR-5(T) is considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium smilacinae sp. nov. is proposed. The type strain is PTYR-5(T) (=CCTCC AB 2013016(T)=KCTC 32300(T)=LMG 27604(T)).

  2. Rhizobium subbaraonis sp. nov., an endolithic bacterium isolated from beach sand.

    PubMed

    Ramana, Ch V; Parag, B; Girija, K R; Ram, B Raghu; Ramana, V Venkata; Sasikala, Ch

    2013-02-01

    Two strains (JC85(T) and JC108) of Gram-stain-negative, motile bacteria were isolated from endolithic beach sand samples on an oligotrophic medium. Based on the 16S rRNA gene sequence analysis, both strains were identified as belonging to the genus Rhizobium. Strain JC108 had 16S rRNA gene sequence similarity of 100 % with Rhizobium pusense NRCPB10(T) and formed a cluster with this strain. Strain JC85(T) had 96.9 % 16S rRNA gene sequence similarity and was 18 % related (based on DNA-DNA hybridization) to Rhizobium borbori DN316(T). With other strains of the genus Rhizobium, the 16S rRNA gene sequence similarity was less than 96.3 %. Strain JC85(T) could tolerate up to 3 % salinity, fix N(2), was resistant to ampicillin (10 µg) and was positive for catalase and oxidase. The major fatty acid was C(18 : 1)ω7c (69 %) with minor amounts of C(19 : 0) cyclo ω8c (8.9 %), C(16 : 0) (6.9 %), C(12 : 0) (5.7 %) and C(19 : 1)ω7c/C(19 : 1)ω6c (2.2 %). Polar lipids of strain JC85(T) include two unidentified aminophospholipids (APL1,2), two unidentified phospholipids (PL1,2), phosphatidylcholine and four unidentified lipids (L1-4). Q-10 is the major quinone of strain JC85(T). Based on polyphasic taxonomic analysis, strain JC85(T) represents a novel species for which, the name Rhizobium subbaraonis JC85(T) is proposed. The type strain is JC85(T) ( = DSM 24765(T) = KCTC 23614(T)).

  3. 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.

  4. Utilization of haem from the haptoglobin-haemoglobin complex by Bacteroides fragilis.

    PubMed

    Otto, B R; Sparrius, M; Wors, D J; de Graaf, F K; MacLaren, D M

    1994-09-01

    Possession of specialized iron acquisition systems is a prerequisite for the survival of pathogenic bacteria in their host. The purpose of this study was to determine whether Bacteroides fragilis, a clinically important Gram-negative anaerobic bacterium, possesses a specific haem-uptake system. Growth studies indicated that this microorganism can utilize haem from either haemoglobin or haptoglobin-haemoglobin as its sole source of iron. Iron-repressible haem-binding protein complexes (HBP complexes), involved in the uptake of haem from haptoglobin-haemoglobin were detected by means of lithium dodecyl sulfate polyacrylamide gel electrophoresis (LDS-PAGE). Four polypeptides of approximately 60, 58, 49 and 35 kDa, which are part of these HBP complexes, were identified as haem-binding proteins. A 44 kDa iron-repressible outer-membrane protein is needed for a functional HBP complex, but the exact role of this protein in the uptake of haem is still unknown.

  5. Symbiotic relationship of Bacteroides cellulosolvens and Clostridium saccharolyticum in cellulose fermentation

    SciTech Connect

    Murray, W.D.

    1986-04-01

    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. cellulosovens exhibited an early cessation of growth which was not due to nutrient depletion, low pH, or toxic accumulation of acetic acid, ethanol, lactic acid, H/sub 2/, CO/sub 2/, 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.

  6. 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

  7. Prevalence and characteristics of nim genes encoding 5-nitroimidazole resistance among Bacteroides strains isolated in Morocco.

    PubMed

    Haggoud, A; M'Hand, R A; Reysset, G; El M'Daghri, N; Benbachir, M; Moumni, M

    2001-01-01

    We report here an evaluation of the dissemination of nim genes, encoding 5-nitroimidazoles resistance, among Bacteroides clinical strains isolated in Morocco. This study was done using a PCR method. Among 60 strains studied, nine contain a copy of a nim gene. The sequence determination of these genes showed that they are homologous to three nim genes previously characterized in strains isolated in France: nimB (five genes), nimC (three genes), and nimA (one gene). Although the nimA and nimC genes were previously identified on plasmids pIP417 and pIP419, respectively, we found here that they have a chromosomal location. The MICs of three 5-nitroimidazole antibiotics (metronidazole, ornidazole, and tinidazole) of the nim gene-containing strains were very low (0.5-2 microg/ml), indicating that the nim genes were not efficiently expressed in these clinical isolates.

  8. A Novel Selective Medium for Isolation of Bacteroides fragilis from Clinical Specimens.

    PubMed

    Ho, Pak-Leung; Ho, Lok-Yan; Yau, Chong-Yee; Tong, Man-Ki; Chow, Kin-Hung

    2017-02-01

    A novel Bacteroides fragilis selective (BFS) medium, consisting of a brain heart infusion agar base supplemented with yeast extract, cysteine hydrochloride, bile salts, vitamin K, hemin, glucose, esculin, ferric ammonium citrate, bromothymol blue, gentamicin, kanamycin, and novobiocin, was evaluated. When BFS agar was tested with a collection of 303 bacteria of different genera, it allowed the growth of B. fragilis as large yellow colonies, with blackening of the medium after 48 h of anaerobic incubation, while the growth of most other anaerobes, facultative anaerobes, and aerobes was inhibited. In a prospective comparison of BFS agar with a routinely used medium (neomycin blood agar) in 1,209 clinical specimens, 60 B. fragilis bacteria were detected on BFS agar while 46 were detected on the routine agar (McNemar's test, P = 0.008). In conclusion, this novel medium may be added to improve the recovery of B. fragilis in clinical specimens and to facilitate surveillance of antimicrobial-resistant strains.

  9. Factors affecting the in vitro activity of cefoperazone against the Bacteroides fragilis group.

    PubMed Central

    Sutter, V L; Kwok, Y Y

    1981-01-01

    The in vitro activity of cefoperazone against 32 strains of bacteria of the Bacteroides fragilis group was determined on four media by using a variety of test parameters. Lower mean minimal inhibitory concentrations (MICs) were obtained on Mueller-Hinton blood agar and supplemented brain heart infusion agar than were obtained on brucella laked blood agar or Wilkins-Chalgren agar. Higher MICs were obtained with 6-h inocula than with 24-h inocula, and slightly higher MICs were obtained with tests read at 48 as compared with 24 h. Conducting tests in an anaerobic glove box had little effect. The greatest differences in mean MICs were seen with inoculum densities of 10(4) and 10(5) colony-forming units. PMID:6459765

  10. The gut commensal Bacteroides thetaiotaomicron exacerbates enteric infection through modification of the metabolic landscape

    PubMed Central

    Curtis, Meredith M.; Hu, Zeping; Klimko, Claire; Narayanan, Sanjeev; Deberardinis, Ralph; Sperandio, Vanessa

    2014-01-01

    SUMMARY The enteric pathogen enterohemorrhagic Escherichia coli (EHEC) causes severe diarrhea but the influence of the gut microbiota on EHEC infection is largely unknown. A predominant member of the microbiota, Bacteroides thetaiotaomicron (Bt), is resident at EHEC attachment sites. We show that Bt enhances EHEC virulence gene expression through the transcription factor, Cra, which is functionally sensitive to sugar concentrations. This enhanced virulence accompanies increased formation of attaching and effacing (AE) lesions requisite for EHEC colonization. Infection with Citrobacter rodentium, a natural mouse pathogen homologous to EHEC, in Bt-reconstituted mice results in increased gut permeability along with exacerbated host pathology and mortality compared to mice deplete of microflora. Bt modifies the metabolite environment at infection sites, increasing metabolites involved in gluconeogenesis, with stark increases in succinate, which can be sensed by Cra. Our findings suggest that microbiota composition affects disease outcome and may explain links between microbiota composition and disease susceptibility. PMID:25498343

  11. 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.

  12. Antimicrobial resistance in the Bacteroides fragilis group in faecal microbiota from healthy Danish children.

    PubMed

    Sydenham, Thomas Vognbjerg; Jensen, Betina Hebbelstrup; Petersen, Andreas Munk; Krogfelt, Karen Angeliki; Justesen, Ulrik Stenz

    2017-03-30

    The Bacteroides fragilis group constitute a significant portion of the human gut microbiota and comprise a major proportion of anaerobic bacteria isolated in human infections. We established a baseline of antimicrobial susceptibility rates in the B. fragilis group in the intestinal tract of relatively antibiotic-naive healthy Danish children. From 174 faecal samples collected from children attending day care, 359 non-duplicate isolates were screened for antimicrobial susceptibility. Of these, 0.0%, 1.9%, 5.0% and 21.2% of isolates were intermediate-susceptible or resistant to metronidazole, meropenem, piperacillin/tazobactam and clindamycin, respectively. Eighteen additional studies reporting susceptibility rates in the B. fragilis group bacteria were identified by conducting a literature search. Heterogeneity among results from studies of B. fragilis group antimicrobial susceptibility rates in faecal microbiota exists.

  13. 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

    2015-10-02

    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.

  14. 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

  15. Fermentation of L-aspartate by a saccharolytic strain of Bacteroides melaninogenicus.

    PubMed Central

    Wong, J C; Dyer, J K; Tribble, J L

    1977-01-01

    Resting cells of Bacteroides melaninogenicus fermented L-[14C]aspartate as a single substrate. The 14C-labeled products included succinate, acetate, CO2, oxaloacetate, formate, malate, glycine, alanine, and fumarate in the relative percentages 68, 15, 9.9, 2.7, 1.8, 1.0, 0.7, 0.5, and 0.06, respectively, based on the total counts per minute of the L-[14C]aspartate fermented. Ammonia was produced in high amounts, indicating that 96% of the L-aspartate fermented was deaminated. These data suggest that L-aspartate is mainly being reduced through a number of intermediate reactions involving enzymes of the tricarboxylic acid cycle to succinate. L-[14C]asparagine was also fermented by resting cells of B. melaninogenicus to form L-aspartate, which was subsequently, but less actively, fermented. PMID:13713

  16. Prior stimulation of antigen-presenting cells with Lactobacillus regulates excessive antigen-specific cytokine responses in vitro when compared with Bacteroides

    PubMed Central

    Tsuda, Masato; Yanagibashi, Tsutomu; Hachimura, Satoshi; Hirayama, Kazuhiro; Itoh, Kikuji; Takahashi, Kyoko; Kaminogawa, Shuichi

    2007-01-01

    The development of allergy is related to differences in the intestinal microbiota. Therefore, it is suggested that the immune responses induced by different genera of bacteria might be regulated through adaptive as well as innate immunity. In this study, we examined whether antigen-specific immune responses were affected by stimulation with the different genera of intestinal bacteria in vitro. Mesenteric lymph node (MLN) cells isolated from germ-free ovalbumin (OVA)-specific T cell receptor transgenic (OVA-Tg) mice were stimulated with OVA and intestinal bacteria. Cecal contents from conventional mice but not germ-free mice could induce OVA-specific cytokine production. Among the murine intestinal bacteria, Bacteroides acidofaciens (BA) enhanced OVA-specific IFN-γ and IL-10 production while Lactobacillusjohnsonii (LA) increased OVA-specific IL-10 production only. The expression of cell surface molecules and cytokine production by antigen-presenting cells (APCs) from germ-free Balb/c mice were analyzed. BA increased the expression of MHC II and co-stimulatory molecules on APCs compared with LA. BA increased IL-6 and IL-10 production but induced less IL-12p40 than LA. To examine the effects of prior stimulation of APCs by intestinal bacteria on the induction of antigen-specific immune responses, cytokine production was determined following co-culture with OVA, CD4+ T cells from OVA-Tg mice, and APCs which were pre-stimulated with the bacteria or not. APCs pre-stimulated with LA did not enhance OVA-specific cytokine production while BA stimulated OVA-specific IL-10 production. These results suggest that the prior stimulation of intestinal immunocytes by Lactobacillus might regulate excessive antigen-specific cytokine responses via APCs when compared with prior stimulation by Bacteroides. PMID:19002998

  17. Metabolism of polyethylene glycol by two anaerobic bacteria, Desulfovibrio desulfuricans and a Bacteroides sp

    SciTech Connect

    Dwyer, D.F.; Tiedje, J.M.

    1986-10-01

    Two anaerobic bacteria were isolated from polyethylene glycol (PEG)-degrading, methanogenic, enrichment cultures obtained from a municipal sludge digester. One isolate, identified as Desulfovibrio desulfuricans (strain DG2), metabolized oligomers ranging from ethylene glycol (EG) to tetraethylene glycol. The other isolate, identified as a Bacteroides sp. (strain PG1), metabolized diethylene glycol and polymers of PEG up to an average molecular mass of 20,000 g/mol (PEG 20000; HO-(CH/sub 2/-CH/sub 2/-O-)/sub n/H). Both strains produced acetaldehyde as an intermediate, with acetate, ethanol, and hydrogen as end products. In coculture with a Methanobacterium sp., the end products were acetate and methane. Polypropylene glycol (HO-(CH/sub 2/-CH/sub 2/-CH/sub 2/-O-)/sub n/H) was not metabolized by either bacterium, and methanogenic enrichments could not be obtained on this substrate. Cell extracts of both bacteria dehydrogenated EG, PEGs up to PEG 400 in size, acetaldehyde, and other mono- and dihydroxylated compounds. Extracts of Bacteroides strain PGI could not dehydrogenate long polymers of PEG (less than or equal to1000 g/mol), but the bacterium grew with PEG 1000 or PEG 20000 as a substrate and therefore possesses a mechanism for PEG depolymerization not present in cell extracts. In contrast, extracts of D. desulfuricans DG2 dehydrogenated long polymers of PEG, but whole cells did not grow with these polymerase substrates. This indicated that the bacterium could not convert PEG to a product suitable for uptake.

  18. 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.

  19. The role of Bacteroides fragilis RecQ DNA helicases in cell survival after metronidazole exposure.

    PubMed

    Paul, Lynthia; Patrick, Sheila; Nord, Carl Erik; Abratt, Valerie

    2011-06-01

    The inactivation of Bacteroides fragilis genes encoding putative RecQ helicases recQ1, recQ2 and recQ3 (ORFs BF638R_3282, BF638R_3781, BF638R_3932) was used to determine whether these proteins are involved in cell survival following metronidazole exposure. The effects of the mutations on growth, cellular morphology and DNA integrity were also evaluated. Mutations in the RecQ DNA helicases caused increased sensitivity to metronidazole, with recQ1, recQ2 and recQ3 mutants being 1.32-fold, 41.88-fold and 23.18-fold more sensitive than the wild type, respectively. There was no difference in cell growth between the recQ1 and recQ3 mutants and the wild type. However, the recQ2 mutant exhibited reduced cell growth, aberrant cell division and increased pleiomorphism, with an increase in filamentous forms and chains of cells being observed using light, fluorescence and electron microscopy. There was no spontaneous accumulation of DNA single- or double-strand breaks in the recQ mutants, as compared with the wild type, during normal cell growth in the absence of metronidazole. Bacteroides fragilis RecQ DNA helicases, therefore, enhance cell survival following metronidazole damage. The abnormal cellular phenotype and growth characteristics of recQ2 mutant cells suggest that this gene, or the downstream gene of the operon in which it occurs, may be involved in cell division.

  20. 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

  1. 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.

  2. Rhizobium phenanthrenilyticum sp. nov., a novel phenanthrene-degrading bacterium isolated from a petroleum residue treatment system.

    PubMed

    Wen, Ya; Zhang, Juan; Yan, Qiuxiang; Li, Shunpeng; Hong, Qing

    2011-01-01

    Strain F11(T), a phenanthrene-degrading bacterium, was isolated from a petroleum residue treatment system, and classified under the genus Rhizobium based on the similarity analysis of its 16S rRNA and recA gene sequences. Strain F11(T) falls into the same phylogenetic clade with Rhizobium oryzae Alt 505(T) (96.8% 16S rRNA gene sequence similarity) and Rhizobium pseudoryzae J34A-127(T) (96.2%). Major cellular fatty acids of strain F11(T) are C(16:0) (6.24%) and summed feature 8 (C(18:1ω7c) and/or C(18:1ω6c), 76.59%), which are also the major fatty acids of R. oryzae Alt 505(T) and R. pseudoryzae J34A-127(T). The DNA G+C content of strain F11(T) was 59.3±0.4 mol%. Based on the phylogenetic analysis as well as biochemical and physiological characteristics, strain F11(T) could be separated from all recognized Rhizobium species. Strain F11(T) (=DSM 21882(T) =CCTCC AB 209029(T)) was considered to be representative of a novel species of Rhizobium, for which the name Rhizobium phenanthrenilyticum sp. nov. is proposed.

  3. Reduction in pathogen populations at grapevine wound sites is associated with the mechanism underlying the biological control of crown gall by rhizobium vitis strain ARK-1.

    PubMed

    Kawaguchi, Akira

    2014-09-17

    A nonpathogenic strain of Rhizobium (=Agrobacterium) vitis, ARK-1, limited the development of grapevine crown gall. A co-inoculation with ARK-1 and the tumorigenic strain VAT07-1 at a 1:1 cell ratio resulted in a higher population of ARK-1 than VAT07-1 in shoots without tumors, but a significantly lower population of ARK-1 than VAT07-1 in grapevine shoots with tumors. ARK-1 began to significantly suppress the VAT07-1 population 2 d after the inoculation. This result indicated that ARK-1 reduced the pathogen population at the wound site through biological control. Although ARK-1 produced a zone of inhibition against other tumorigenic Rhizobium spp. in in vitro assays, antibiosis depended on the culture medium. ARK-1 did not inhibit the growth of tumorigenic R. radiobacter strain AtC1 in the antibiosis assay, but suppressed the AtC1-induced formation of tumors on grapevine shoots, suggesting that antibiosis by ARK-1 may not be the main mechanism responsible for biological control.

  4. Life in an arsenic-containing gold mine: genome and physiology of the autotrophic arsenite-oxidizing bacterium rhizobium sp. NT-26.

    PubMed

    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.

  5. 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

  6. Identification of Rhizobium spp. in peat-based inoculants by DNA hybridization and PCR and its application in inoculant quality control.

    PubMed Central

    Tas, E; Saano, A; Leinonen, P; Lindström, K

    1995-01-01

    Procedures based on DNA hybridization and PCR were developed for quality control of Rhizobium inoculants. Inoculants for pea and goat's rue were produced by Elomestari Ltd., Juva, Finland, in sterile dry fine peat by the standard procedure used by the company. The inoculants contained Rhizobium galegae HAMBI 1174 and HAMBI 1207 and an R. leguminosarum biovar vicia strain, 16HSA, either solely or in combinations of two or three strains. DNA was isolated from 1-g samples of each peat inoculant and analyzed by nonradioactive DNA-DNA hybridization and by PCR. The hybridization probes were total DNAs from pure cultures of R. galegae HAMBI 1207 and R. leguminosarum biovar viciae 16HSA and a 264-bp strain-specific fragment from the genome of R. galegae HAMBI 1174. The total DNA probes distinguished inoculants containing R. galegae or R. leguminosarum, and the strain-specific probe distinguished inoculants containing R. galegae HAMBI 1174. The hybridization results for R. galegae were verified in a PCR experiment by amplifying an R. galegae species-specific fragment and an R. galegae HAMBI 1174 strain-specific fragment in the same reaction. When suitable probes and primers are available, the methods described here offer promising alternatives for the quality control of peat-based inoculants. PMID:7646020

  7. Reduction in Pathogen Populations at Grapevine Wound Sites is Associated with the Mechanism Underlying the Biological Control of Crown Gall by Rhizobium vitis Strain ARK-1

    PubMed Central

    Kawaguchi, Akira

    2014-01-01

    A nonpathogenic strain of Rhizobium (=Agrobacterium) vitis, ARK-1, limited the development of grapevine crown gall. A co-inoculation with ARK-1 and the tumorigenic strain VAT07-1 at a 1:1 cell ratio resulted in a higher population of ARK-1 than VAT07-1 in shoots without tumors, but a significantly lower population of ARK-1 than VAT07-1 in grapevine shoots with tumors. ARK-1 began to significantly suppress the VAT07-1 population 2 d after the inoculation. This result indicated that ARK-1 reduced the pathogen population at the wound site through biological control. Although ARK-1 produced a zone of inhibition against other tumorigenic Rhizobium spp. in in vitro assays, antibiosis depended on the culture medium. ARK-1 did not inhibit the growth of tumorigenic R. radiobacter strain AtC1 in the antibiosis assay, but suppressed the AtC1-induced formation of tumors on grapevine shoots, suggesting that antibiosis by ARK-1 may not be the main mechanism responsible for biological control. PMID:25077443

  8. Bacteroides induce higher IgA production than Lactobacillus by increasing activation-induced cytidine deaminase expression in B cells in murine Peyer's patches.

    PubMed

    Yanagibashi, Tsutomu; Hosono, Akira; Oyama, Akihito; Tsuda, Masato; Hachimura, Satoshi; Takahashi, Yoshimasa; Itoh, Kikuji; Hirayama, Kazuhiro; Takahashi, Kyoko; Kaminogawa, Shuichi

    2009-02-01

    The gut mucosal immune system is crucial in host defense against infection by pathogenic microbacteria and viruses via the production of IgA. Previous studies have shown that intestinal commensal bacteria enhance mucosal IgA production. However, it is poorly understood how these bacteria induce IgA production and which genera of intestinal commensal bacteria induce IgA production effectively. In this study, we compared the immunomodulatory effects of Bacteroides and Lactobacillus on IgA production by Peyer's patches lymphocytes. IgA production by Peyer's patches lymphocytes co-cultured with Bacteroides was higher than with Lactobacillus. In addition, the expression of activation-induced cytidine deaminase increased in co-culture with Bacteroides but not with Lactobacillus. We found that intestinal commensal bacteria elicited IgA production. In particular, Bacteroides induced the differentiation of Peyer's patches B cell into IgA(+) B cells by increasing activation-induced cytidine deaminase expression.

  9. First genomic analysis of the broad-host-range Rhizobium sp. LPU83 strain, a member of the low-genetic diversity Oregon-like Rhizobium sp. group.

    PubMed

    Tejerizo, Gonzalo Torres; Del Papa, María Florencia; Draghi, Walter; Lozano, Mauricio; Giusti, María de Los Ángeles; Martini, Carla; Salas, María Eugenia; Salto, Ileana; Wibberg, Daniel; Szczepanowski, Rafael; Weidner, Stefan; Schlüter, Andreas; Lagares, Antonio; Pistorio, Mariano

    2011-08-20

    Alfalfa (Medicago sativa) is the most cultivated forage legume for cattle and animal feeding, occupying about 32 million hectares over the world. Management of the N₂-fixing symbiosis of this plant to maximize crop production is therefore an important objective. A fundamental constraint to this aim emerges when a moderately low soil pH hampers the establishment of an effective symbiosis with indigenous and/or inoculated rhizobia. Besides the association of alfalfa with Ensifer (Sinorhizobium) meliloti, this legume is able to establish a symbiosis with Ensifer (Sinorhizobium) medicae and with less characterized types of rhizobia, such as the Oregon-like strains, Rhizobium sp. Or191 initially isolated in the USA, and the Rhizobium sp. LPU83 strain, from Argentina. These strains are acid-tolerant, highly competitive for acidic-soil-alfalfa nodulation, but inefficient for biological nitrogen fixation with alfalfa. These features position the Oregon-like rhizobia as strains of potential risk in agricultural soils compared with the efficient symbiont E. meliloti. Moreover, the collected genetic information has revealed that the genomic structure of these rhizobial isolates is complex in terms of sequence similarities shared with other rhizobia. Such a "patched" genetic composition has obviously imposed severe restrictions to the classical taxonomy of these rhizobia. In this work we summarize the accumulated knowledge about the Oregon-like rhizobia and present a phylogenetic analysis based on genome sequence data of Rhizobium sp. LPU83 obtained by a high-throughput sequencing on the Genome Sequencer FLX Titanium platform. The accessibility of the complete genomic sequence will release up more experimental possibilities since this information will then enable biochemical studies as well as proteomics and transcriptomics approaches.

  10. Comparative antimicrobial efficacy of Metapex, Metronidazole, BioPure MTAD, Aztreonam on Bacteroides fragilis and Propionibacterium acne

    PubMed Central

    Balakrishnan, Rajkumar; Dubey, Sandeep; Dhole, Tapan Kumar N; Boruah, Lalit C; Srivastava, Sanjeev

    2013-01-01

    Aim: The purpose of this study was to evaluate the comparative antibacterial efficacy of Biopure MTAD, Metapex, Metronidazole, and Aztreonam against two obligate anerobic bacteria. Materials and Methods: Antimicrobial efficacy of selected medicaments against two obligate anaerobic bacteria Bacteroides fragilis and Propionibacterium acnes was done by Agar disc-diffusion method. Pre-sterilized Whatman paper discs, 6 mm in diameter and soaked with the test solution, were prepared and placed onto the previously seeded agar Petri plates. Each plate was incubated in anaerobic jar for anerobic environment at 37°C for 48 hours. A zone of inhibition was recorded for each plate and the results were analysed statistically. Saline and ethanol used as control group in this study. Results: Biopure MTAD, Metapex and Metronidazole were effective against all the selected microorganisms. Aztreonam was effective against Bacteroides fragilis. Saline and ethanol used as control were ineffective. Conclusions: Metronidazole showed the superior antibacterial property amongst the tested medicaments. PMID:23956535

  11. Selection for cheating across disparate environments in the legume-rhizobium mutualism.

    PubMed

    Porter, Stephanie S; Simms, Ellen L

    2014-09-01

    The primary dilemma in evolutionarily stable mutualisms is that natural selection for cheating could overwhelm selection for cooperation. Cheating need not entail parasitism; selection favours cheating as a quantitative trait whenever less-cooperative partners are more fit than more-cooperative partners. Mutualisms might be stabilised by mechanisms that direct benefits to more-cooperative individuals, which counter selection for cheating; however, empirical evidence that natural selection favours cheating in mutualisms is sparse. We measured selection on cheating in single-partner pairings of wild legume and rhizobium lineages, which prevented legume choice. Across contrasting environments, selection consistently favoured cheating by rhizobia, but did not favour legumes that provided less benefit to rhizobium partners. This is the first simultaneous measurement of selection on cheating across both host and symbiont lineages from a natural population. We empirically confirm selection for cheating as a source of antagonistic coevolutionary pressure in mutualism and a biological dilemma for models of cooperation.

  12. Rhizobium strains differ considerably in outer membrane permeability and polymyxin B resistance.

    PubMed

    Komaniecka, Iwona; Zamłyńska, Katarzyna; Zan, Radosław; Staszczak, Magdalena; Pawelec, Jarosław; Seta, Irena; Choma, Adam

    2016-01-01

    Six rhizobium (Rhizobium leguminosarum bv. Trifolii TA1, Sinorhizobium meliloti 1021, Mesorhizobium huakuii IFO 15243(T), Ochrobactrum lupini LUP 21(T), Bradyrhizobium japonicum USDA110 and B. elkanii USDA 76) and two Escherichia coli strains (E. coli ATCC 25922 and E. coli HB 101) were compared in respect to polymyxin B and EDTA resistance, as well as bacterial outer membrane (OM) permeability to a fluorescent hydrophobic agent (N-phenyl-1-naphthylamine - NPN). TEM (Transmission Electron Microscopy) and a microbial test demonstrated that all the rhizobia were much more resistant to polymyxin B in comparison with E. coli strains. EDTA and polymyxin B enhance permeability of B. japonicum and O. lupini OM. Other rhizobia incorporated NPN independently of the presence of membrane-deteriorating agents; however, the level of fluorescence (measured as NPN absorption) was strain dependent.

  13. 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

  14. Use of Two-Dimensional Polyacrylamide Gel Electrophoresis to Identify and Classify Rhizobium Strains

    PubMed Central

    Roberts, Gary P.; Leps, Walter T.; Silver, Lin E.; Brill, Winston J.

    1980-01-01

    Fifty-seven strains of various Rhizobium species were analyzed by two-dimensional gel electrophoresis. Since the protein pattern on such gels is a reflection of the genetic background of the tested strains, similarities in pattern allowed us to estimate the relatedness between these strains. All group II rhizobia (slow growing) were closely related and were very distinct from group I rhizobia (fast growing). Rhizobium meliloti strains formed a distinct group. The collection of R. leguminosarum and R. trifolii strains together formed another distinct group. Although there were some similarities within the R. phaseoli, sesbania rhizobia, and lotus rhizobia, the members within these seemed much more diverse than the members of the above groups. The technique also is useful to determine whether two unknown strains are identical. Images PMID:16345514

  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. Compositional studies on succinoglycan-like extracellular water-soluble Rhizobium polysaccharides.

    PubMed

    Ghai, S K

    1981-01-01

    This study reports structural information on extracellular, water-soluble polysaccharides from 5 different strains of Rhizobium, viz. R. trifolii J60, R. meliloti J1017, 202, 204 and 207. All the 5 polysaccharides had glucose and galactose in approximate molar ratio of 7:1. Methylation analysis revealed that the polysaccharides contained (1 leads to 3), (1 leads to 6), (1 leads to 4), (1 leads to 4, 1 leads to 6)-linked D-glucose residues, (1 leads to 3)-linked D-galactose and non-reducing terminal D-glucose attached to pyruvate. This structure was found to be exactly the same as that of succinoglycan, a succinic acid containing water-soluble polysaccharide elaborated by Alcaligenes faecalis var. myxogenes 10C3. The similarity of the structure of polysaccharides of two different Rhizobium species and also to the polysaccharide produced by Alcaligenes are discussed in terms of host specificity.

  17. Characterization of new exopolysaccharide production by Rhizobium tropici during growth on hydrocarbon substrate.

    PubMed

    Castellane, Tereza Cristina Luque; Campanharo, João Carlos; Colnago, Luiz Alberto; Coutinho, Isabel Duarte; Lopes, Érica Mendes; Lemos, Manoel Victor Franco; de Macedo Lemos, Eliana Gertrudes

    2017-03-01

    Exopolysaccharide (EPS) are produced by a diverse of rhizobia species and has been demonstrated to be a bioemulsifier with potential applications in the degradation of hydrocarbons. In the present study, attempts were made to obtain the new exopolysaccharide production by Rhizobium tropici (SEMIA 4080 and MUTZC3) strains during growth on hydrocarbon substrate. Under the different cultivation conditions, the high molecular weight exopolysaccharides from Rhizobium tropici strains cultivated for 96h mainly consisted of carbohydrates (79-85%) and a low percentage of protein. The EPSC3-D differed from the others, with only 60% of carbohydrate. However, all strains produced polymers with distinct rheology properties, such as viscosity of each EPS sample, suitable for different applications. In addition, RP-HPLC, FTIR and NMR studies revealed EPS produced by rhizobia strains were similar indicating minimal difference between EPS compositions.

  18. Enumeration of polysaccharide-degrading Bacteroides species in human feces by using species-specific DNA probes.

    PubMed Central

    Kuritza, A P; Shaughnessy, P; Salyers, A A

    1986-01-01

    DNA probes that are specific for each of five predominant species of human colonic Bacteroides (B. thetaiotaomicron, B. uniformis, B. distasonis, "Bacteroides group 3452-A", and B. ovatus) were used to detect and enumerate these species in fecal samples from two adult volunteers. These five species are capable of fermenting many of the complex polysaccharides that are thought to be sources of carbon and energy for bacteria in the colon. Estimates for the concentrations of some of these species in feces have not been previously available because of the difficulties in differentiating colonic Bacteroides spp. by conventional biochemical tests. Our results indicate that all the species except B. ovatus were present in high numbers (greater than 10(9)/g [dry weight]) in the feces of both volunteers. However, the concentrations of the more versatile polysaccharide-degrading species within this group of organisms (7.6 X 10(9) to 12.0 X 10(9)/g [dry weight] for B. thetaiotaomicron; 2.9 X 10(9) to 6.3 X 10(9)/g [dry weight] for "Bacteroides group 3452-A") did not differ significantly from the concentrations of less versatile polysaccharide-degrading species (1.2 X 10(10) to 2.0 X 10(10)/g [dry weight] for B. uniformis; 5.8 X 10(9) to 8.4 X 10(9)/g [dry weight] for B. distasonis). B. ovatus was not detectable by our method. Since our lower limit of detection is approximately 1 X 10(9) to 2 X 10(9)/g (dry weight) of feces, this is consistent with earlier estimates that indicated that the concentration of B. ovatus in feces is near or below this value.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:3954350

  19. Enumeration of polysaccharide-degrading Bacteroides species in human feces by using species-specific DNA probes.

    PubMed

    Kuritza, A P; Shaughnessy, P; Salyers, A A

    1986-02-01

    DNA probes that are specific for each of five predominant species of human colonic Bacteroides (B. thetaiotaomicron, B. uniformis, B. distasonis, "Bacteroides group 3452-A", and B. ovatus) were used to detect and enumerate these species in fecal samples from two adult volunteers. These five species are capable of fermenting many of the complex polysaccharides that are thought to be sources of carbon and energy for bacteria in the colon. Estimates for the concentrations of some of these species in feces have not been previously available because of the difficulties in differentiating colonic Bacteroides spp. by conventional biochemical tests. Our results indicate that all the species except B. ovatus were present in high numbers (greater than 10(9)/g [dry weight]) in the feces of both volunteers. However, the concentrations of the more versatile polysaccharide-degrading species within this group of organisms (7.6 X 10(9) to 12.0 X 10(9)/g [dry weight] for B. thetaiotaomicron; 2.9 X 10(9) to 6.3 X 10(9)/g [dry weight] for "Bacteroides group 3452-A") did not differ significantly from the concentrations of less versatile polysaccharide-degrading species (1.2 X 10(10) to 2.0 X 10(10)/g [dry weight] for B. uniformis; 5.8 X 10(9) to 8.4 X 10(9)/g [dry weight] for B. distasonis). B. ovatus was not detectable by our method. Since our lower limit of detection is approximately 1 X 10(9) to 2 X 10(9)/g (dry weight) of feces, this is consistent with earlier estimates that indicated that the concentration of B. ovatus in feces is near or below this value.(ABSTRACT TRUNCATED AT 250 WORDS)

  20. 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%.

  1. Isolation and reconstitution of iron- and manganese-containing superoxide dismutases from Bacteroides thetaiotaomicron.

    PubMed Central

    Pennington, C D; Gregory, E M

    1986-01-01

    Superoxide dismutase (SOD) from extracts of anaerobically maintained Bacteroides thetaiotaomicron was a dimer of equally sized 23,000-molecular-weight monomers joined noncovalently. A preparation with a specific activity of 1,200 U/mg contained 1.1 g-atom of Fe, 0.6 g-atom of Zn, and less than 0.05 g-atom of Mn per mol of dimer. The apoprotein, prepared by dialysis of iron-SOD in 5 M guanidinium chloride-20 mM 8-hydroxyquinoline, had no superoxide-scavenging activity when renatured without exogenous metal. Enzymatic activity was restored to the denatured apoprotein by dialysis against either 1 mM Fe(NH4)2 or 1 mM MnCl2 in 20 mM Tris (pH 7.0). The Fe-reconstituted enzyme and the native enzyme were inhibited approximately 50% by 0.2 mM NaN3, whereas the Mn-reconstituted enzyme was inhibited 60% by 10 mM NaN3. Aeration of the anaerobic cells resulted in a fourfold induction of an azide-resistant SOD. The enzyme (43,000 molecular weight) isolated from aerated cells was a dimer of equally sized subunits. The metal content was 1.0 g-atom of Mn, 0.55 g-atom of Fe, and 0.3 g-atom of Zn per mol of dimer. Enzymatic activity of the denatured apoprotein from this enzyme was also restored on addition of either iron or manganese. The constitutive Fe-SOD and the O2-induced Mn-SOD, tested alone and in combination, migrated identically on acrylamide gels, had similar amino acid compositions, and had alanine as the sole N-terminal amino acid. These data are consistent with the synthesis of a single apoprotein in either anaerobically maintained or oxygenated cells. We have observed a similar phenomenon with SOD from Bacteroides fragilis (E. M. Gregory, Arch. Biochem. Biophys. 238:83-89, 1985). PMID:3700336

  2. Characterization of the nodulation plasmid encoded chemoreceptor gene mcpG from Rhizobium leguminosarum

    PubMed Central

    Yost, Christopher K; Clark, Kirsten T; Del Bel, Kate L; Hynes, Michael F

    2003-01-01

    Background In general, chemotaxis in Rhizobium has not been well characterized. Methyl accepting chemotaxis proteins are sensory proteins important in chemotaxis of numerous bacteria, but their involvement in Rhizobium chemotaxis is unclear and merits further investigation. Results A putative methyl accepting chemotaxis protein gene (mcpG) of Rhizobium leguminosarum VF39SM was isolated and characterized. The gene was found to reside on the nodulation plasmid, pRleVF39d. The predicted mcpG ORF displayed motifs common to known methyl-accepting chemotaxis proteins, such as two transmembrane domains and high homology to the conserved methylation and signaling domains of well-characterized MCPs. Phenotypic analysis of mcpG mutants using swarm plates did not identify ligands for this putative receptor. Additionally, gene knockouts of mcpG did not affect a mutant strain's ability to compete for nodulation with the wild type. Notably, mcpG was found to be plasmid-encoded in all strains of R. leguminosarum and R. etli examined, though it was found on the nodulation plasmid only in a minority of strains. Conclusions Based on sequence homology R. leguminosarum mcpG gene codes for a methyl accepting chemotaxis protein. The gene is plasmid localized in numerous Rhizobium spp. Although localized to the sym plasmid of VF39SM mcpG does not appear to participate in early nodulation events. A ligand for McpG remains to be found. Apparent McpG orthologs appear in a diverse range of proteobacteria. Identification and characterization of mcpG adds to the family of mcp genes already identified in this organism. PMID:12553885

  3. Rhizobium borbori sp. nov., aniline-degrading bacteria isolated from activated sludge.

    PubMed

    Zhang, Guo Xia; Ren, Sui Zhou; Xu, Mei Ying; Zeng, Guo Qu; Luo, Hui Dong; Chen, Jin Lin; Tan, Zhi Yuan; Sun, Guo Ping

    2011-04-01

    Three aniline-degrading bacteria, strains DN316(T), DN316-1 and DN365, were isolated from activated sludge. According to 16S rRNA gene sequence-based phylogenetic analysis, the isolates belonged to the genus Rhizobium, with Rhizobium ( = Agrobacterium) radiobacter LMG 140(T) as the closest relative, with 96.5 % sequence similarity. Phylogenetic analysis of the representative strain DN316(T) using sequences of the glnA, thrC and recA genes and the 16S-23S intergenic spacer region confirmed the phylogenetic arrangement obtained from analysis of the 16S rRNA gene. DNA-DNA relatedness between DN316(T) and R. radiobacter LMG 140(T) was 43.7 %, clearly indicating that the representative strain DN316(T) represents a novel species. Phenotypic and biochemical characterization of the isolates and insertion sequence-PCR fingerprinting patterns showed several distinctive features that differentiated them from closely related species. The major components of the cellular fatty acids were C(18 : 1)ω7c (57.10 %), C(16 : 0) (11.31 %) and C(19 : 0) cyclo ω8c (10.13 %). Based on our taxonomic analysis, the three isolates from activated sludge represent a novel species of the genus Rhizobium, for which the name Rhizobium borbori sp. nov. is proposed. The type strain is DN316(T) ( = CICC 10378(T)  = LMG 23925(T)).

  4. Rhizobium giardinii is the microsymbiont of Illinois bundleflower (Desmanthus illinoensis (Michx.) Macmillan) in midwestern prairies.

    PubMed

    Beyhaut, Elena; Tlusty, Becki; van Berkum, Peter; Graham, Peter H

    2006-09-01

    Illinois bundleflower (Desmanthus illinoensis (Michx.) Macmillan) has potential as a grain and forage legume for the American Midwest. Inoculant-quality rhizobia for this legume have been identified but not previously characterized. Rhizobia trapped from 20 soils in the natural range of the Illinois bundleflower had characteristics that placed them overwhelmingly within the species Rhizobium giardinii, one of the few occasions this species has been recovered from legumes, raising questions on the biogeography and spread of midwestern prairie rhizobia.

  5. The contribution of bacteroidal nitrate and nitrite reduction to the formation of nitrosylleghaemoglobin complexes in soybean root nodules.

    PubMed

    Meakin, Georgina E; Bueno, Emilio; Jepson, Brian; Bedmar, Eulogio J; Richardson, David J; Delgado, María J

    2007-02-01

    It is becoming recognized that leghaemoglobin constitutes an important buffer for the cytotoxic nitric oxide radical (NO(*)) in root nodules, although the sources of this NO(*) within nodules are unclear. In Bradyrhizobium japonicum bacteroids, NO(*) can be produced through the denitrification process, during which nitrate is reduced to nitrite by the periplasmic nitrate reductase Nap, and nitrite is reduced to NO(*) by the respiratory nitrite reductase NirK. To assess the contribution of bacteroidal denitrification to the NO(*) within nitrate-treated soybean nodules, electron paramagnetic resonance and UV-visible spectroscopy were employed to study the presence of nitrosylleghaemoglobin (LbNO) within nodules from plants inoculated with wild-type, napA or nirK B. japonicum strains. Since it has been found that hypoxia induces NO(*) production in plant root tissue, and that plant roots can be subjected to hypoxic stress during drought and flooding, the effect of hypoxic stress on the formation of LbNO complexes within nodules was also investigated. Maximal levels of LbNO were observed in nodules from plants treated with nitrate and subjected to hypoxic conditions. It is shown that, in the presence of nitrate, all of the LbNO within normoxic nodules arises from nitrate reduction by the bacteroidal periplasmic nitrate reductase, whereas Nap activity is only responsible for half of the LbNO within hypoxic nodules. In contrast to Nap, NirK is not essential for LbNO formation under any condition tested.

  6. Intra- and interspecies transfer and expression of Rhizobium japonicum hydrogen uptake genes and autotrophic growth capability

    PubMed Central

    Lambert, Grant R.; Cantrell, Michael A.; Hanus, F. Joe; Russell, Sterling A.; Haddad, Karen R.; Evans, Harold J.

    1985-01-01

    Cosmids containing hydrogen uptake genes have previously been isolated in this laboratory. Four new cosmids that contain additional hup gene(s) have now been identified by conjugal transfer of a Rhizobium japonicum 122DES gene bank into a Tn5-generated Hup- mutant and screening for the acquisition of Hup activity. The newly isolated cosmids, pHU50-pHU53, contain part of the previously isolated pHU1 but extend as far as 20 kilobases beyond its border. pHU52 complements five of six Hup- mutants and confers activity on several Hup- wild-type R. japonicum strains in the free-living state and where tested in nodules. Transconjugants obtained from interspecies transfer of pHU52 to Rhizobium meliloti 102F28, 102F32, and 102F51 and Rhizobium leguminosarum 128C53 showed hydrogen-dependent methyleneblue reduction, performed the oxyhydrogen reaction, and showed hydrogen-dependent autotrophic growth by virtue of the introduced genes. The identity of the presumptive transconjugants was confirmed by antibiotic-resistance profiles and by plant nodulation tests. Images PMID:16578786

  7. 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.

  8. 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)).

  9. Elucidation of the 3-O-deacylase gene, pagL, required for the removal of primary β-hydroxy fatty acid from the lipid A in the nitrogen-fixing endosymbiont Rhizobium etli CE3.

    PubMed

    Brown, Dusty B; Muszynski, Artur; Salas, Omar; Speed, Kacie; Carlson, Russell W

    2013-04-26

    Until now, the gene responsible for the 3-O-deacylation of lipid A among nitrogen-fixing endosymbionts has not been characterized. Several Gram-negative animal pathogens such as Salmonella enterica, Pseudomonas aeruginosa, and Bordetella bronchiseptica contain an outer membrane 3-O-deacylase (PagL) that has been implicated in host immune evasion. The role of 3-O-deacylated lipid A among nitrogen-fixing endosymbionts, plant endophytes, and plant pathogens has not been studied. However, D'Haeze et al. (D'Haeze, W., Leoff, C., Freshour, G., Noel, K. D., and Carlson, R. W. (2007) J. Biol. Chem. 282, 17101-17113) reported that the lipopolysaccharide from Rhizobium etli CE3 bacteroids isolated from host bean root nodules contained exclusively tetraacylated lipid A that lacked a lipid A β-hydroxymyristyl residue, an observation that is consistent with the possibility of PagL activity being important in symbiosis. A putative pagL gene was identified in the R. etli genome sequence. With this information, we created a pagL(-) mutant strain derived from R. etli CE3. Using mass spectrometry, we demonstrated that the mutant lacks 3-O-deacylated lipid A. The parent and mutant LPS were very similar as determined by gel electrophoresis and glycosyl composition analysis using gas chromatography/mass spectrometry. However, fatty acid analysis showed that the mutant lipid A contained larger amounts of β-hydroxypentadecanoic acid than that of the parent. Furthermore, the mutant was adversely affected in establishing symbiosis with its host, Phaseolus vulgaris.

  10. Rhizobium etli and Rhizobium gallicum nodulate common bean (Phaseolus vulgaris) in a traditionally managed milpa plot in Mexico: population genetics and biogeographic implications.

    PubMed

    Silva, Claudia; Vinuesa, Pablo; Eguiarte, Luis E; Martínez-Romero, Esperanza; Souza, Valeria

    2003-02-01

    The stability of the genetic structure of rhizobial populations nodulating Phaseolus vulgaris cultivated in a traditionally managed milpa plot in Mexico was studied over three consecutive years. The set of molecular markers analyzed (including partial rrs, glnII, nifH, and nodB sequences), along with host range experiments, placed the isolates examined in Rhizobium etli bv. phaseoli and Rhizobium gallicum bv. gallicum. Cluster analysis of multilocus enzyme electrophoresis and plasmid profile data separated the two species and identified numerically dominant clones within each of them. Population genetic analyses showed that there was high genetic differentiation between the two species and that there was low intrapopulation differentiation of the species over the 3 years. The results of linkage disequilibrium analyses are consistent with an epidemic genetic structure for both species, with frequent genetic exchange taking place within conspecific populations but not between the R. etli and R. gallicum populations. A subsample of isolates was selected and used for 16S ribosomal DNA PCR-restriction fragment length polymorphism analysis, nifH copy number determination, and host range experiments. Plasmid profiles and nifH hybridization patterns also revealed the occurrence of lateral plasmid transfer among distinct multilocus genotypes within species but not between species. Both species were recovered from nodules of the same plants, indicating that mechanisms other than host, spatial, or temporal isolation may account for the genetic barrier between the species. The biogeographic implications of finding an R. gallicum bv. gallicum population nodulating common bean in America are discussed.

  11. Purification and characterization of an immunoglobulin A1 protease from Bacteroides melaninogenicus.

    PubMed Central

    Mortensen, S B; Kilian, M

    1984-01-01

    Attention has recently been focused on bacterial proteases with the capacity to cleave immunoglobulin A (IgA proteases) as possible pathogenic factors in bacterial meningitis, gonorrhoea, and destructive periodontal disease. Here, we describe a method for the rapid purification of a specific IgA1 protease from Bacteroides melaninogenicus. The IgA1 protease was purified 6,172-fold with a yield of 9% by ammonium sulfate precipitation, DEAE-ion exchange chromatography, and separation on a preparative TSK-G 3000SWG high-pressure gel permeation chromatography column. The enzyme was specific for human IgA1 and cleaved a prolyl-seryl peptide bond in the hinge region of the alpha 1 chain between residues 223 and 224. The molecular weight of the enzyme was 62,000, the isoelectric point was 5.0, and the Km was 3.4 X 10(-6). The enzyme was active over a broad pH range and had maximal activity at pH 5.0. B. melaninogenicus IgA1 protease was classified as a thiol protease on the basis of its inhibition by traditional protease inhibitors and the fact that it was active only under reducing conditions. Images PMID:6147309

  12. Polyamine catabolism contributes to enterotoxigenic Bacteroides fragilis-induced colon tumorigenesis.

    PubMed

    Goodwin, Andrew C; Destefano Shields, Christina E; Wu, Shaoguang; Huso, David L; Wu, XinQun; Murray-Stewart, Tracy R; Hacker-Prietz, Amy; Rabizadeh, Shervin; Woster, Patrick M; Sears, Cynthia L; Casero, Robert A

    2011-09-13

    It is estimated that the etiology of 20-30% of epithelial cancers is directly associated with inflammation, although the direct molecular events linking inflammation and carcinogenesis are poorly defined. In the context of gastrointestinal disease, the bacterium enterotoxigenic Bacteroides fragilis (ETBF) is a significant source of chronic inflammation and has been implicated as a risk factor for colorectal cancer. Spermine oxidase (SMO) is a polyamine catabolic enzyme that is highly inducible by inflammatory stimuli resulting in increased reactive oxygen species (ROS) and DNA damage. We now demonstrate that purified B. fragilis toxin (BFT) up-regulates SMO in HT29/c1 and T84 colonic epithelial cells, resulting in SMO-dependent generation of ROS and induction of γ-H2A.x, a marker of DNA damage. Further, ETBF-induced colitis in C57BL/6 mice is associated with increased SMO expression and treatment of mice with an inhibitor of polyamine catabolism, N(1),N(4)-bis(2,3-butandienyl)-1,4-butanediamine (MDL 72527), significantly reduces ETBF-induced chronic inflammation and proliferation. Most importantly, in the multiple intestinal neoplasia (Min) mouse model, treatment with MDL 72527 reduces ETBF-induced colon tumorigenesis by 69% (P < 0.001). The results of these studies indicate that SMO is a source of bacteria-induced ROS directly associated with tumorigenesis and could serve as a unique target for chemoprevention.

  13. Polyamine catabolism contributes to enterotoxigenic Bacteroides fragilis-induced colon tumorigenesis

    PubMed Central

    Goodwin, Andrew C.; Shields, Christina E. Destefano; Wu, Shaoguang; Huso, David L.; Wu, XinQun; Murray-Stewart, Tracy R.; Hacker-Prietz, Amy; Rabizadeh, Shervin; Woster, Patrick M.; Sears, Cynthia L.; Casero, Robert A.

    2011-01-01

    It is estimated that the etiology of 20–30% of epithelial cancers is directly associated with inflammation, although the direct molecular events linking inflammation and carcinogenesis are poorly defined. In the context of gastrointestinal disease, the bacterium enterotoxigenic Bacteroides fragilis (ETBF) is a significant source of chronic inflammation and has been implicated as a risk factor for colorectal cancer. Spermine oxidase (SMO) is a polyamine catabolic enzyme that is highly inducible by inflammatory stimuli resulting in increased reactive oxygen species (ROS) and DNA damage. We now demonstrate that purified B. fragilis toxin (BFT) up-regulates SMO in HT29/c1 and T84 colonic epithelial cells, resulting in SMO-dependent generation of ROS and induction of γ-H2A.x, a marker of DNA damage. Further, ETBF-induced colitis in C57BL/6 mice is associated with increased SMO expression and treatment of mice with an inhibitor of polyamine catabolism, N1,N4-bis(2,3-butandienyl)-1,4-butanediamine (MDL 72527), significantly reduces ETBF-induced chronic inflammation and proliferation. Most importantly, in the multiple intestinal neoplasia (Min) mouse model, treatment with MDL 72527 reduces ETBF-induced colon tumorigenesis by 69% (P < 0.001). The results of these studies indicate that SMO is a source of bacteria-induced ROS directly associated with tumorigenesis and could serve as a unique target for chemoprevention. PMID:21876161

  14. Purification and properties of hemagglutinin from culture supernatant of Bacteroides gingivalis.

    PubMed Central

    Okuda, K; Yamamoto, A; Naito, Y; Takazoe, I; Slots, J; Genco, R J

    1986-01-01

    The hemagglutinating factor (hemagglutinin) of Bacteroides gingivalis was prepared from the supernatant of a 5-day diffusate broth culture by ammonium sulfate precipitation and column chromatography with a hydrophobic column of Phenyl-Sepharose CL-4B, DEAE-Sephadex A-50, and Sephadex G-100 gel filtration. The hemagglutinating activity of the preparation was 53.3 times higher than that of ammonium sulfate precipitate. In electron microphotographs, hemagglutinin appears to have a vesicle or tubelike structure. The hemagglutinating activity of intact cells was completely destroyed by heating at 100 degrees C for 10 min, but the activity of extracted hemagglutinin was heat stable. The activity of hemagglutinin was inhibited by L-arginine and L-lysine and partially inhibited by phospholipase D, but it was not affected by proteolytic enzymes, neuraminidase, hyaluronidase, lipase, phospholipase A and C, or sugars. The B. gingivalis hemagglutinin appeared to be comprised mainly of a 40,000-molecular-weight material. The Fab fragment of immunoglobulin G prepared from rabbit antiserum to whole cells of B. gingivalis and monoclonal antibody against the hemagglutinin bound to the cell surface and inhibited the hemagglutinating activity of both the cells and the purified hemagglutinin. Images PMID:3781621

  15. Structural and Functional Insights into the Unwinding Mechanism of Bacteroides sp Pif1.

    PubMed

    Zhou, Xianglian; Ren, Wendan; Bharath, Sakshibeedu R; Tang, Xuhua; He, Yang; Chen, Chen; Liu, Zhou; Li, Dewang; Song, Haiwei

    2016-03-01

    Pif1 is a conserved SF1B DNA helicase involved in maintaining genome stability through unwinding double-stranded DNAs (dsDNAs), DNA/RNA hybrids, and G quadruplex (G4) structures. Here, we report the structures of the helicase domain of human Pif1 and Bacteroides sp Pif1 (BaPif1) in complex with ADP-AlF4(-) and two different single-stranded DNAs (ssDNAs). The wedge region equivalent to the β hairpin in other SF1B DNA helicases folds into an extended loop followed by an α helix. The Pif1 signature motif of BaPif1 interacts with the wedge region and a short helix in order to stabilize these ssDNA binding elements, therefore indirectly exerting its functional role. Domain 2B of BaPif1 undergoes a large conformational change upon concomitant binding of ATP and ssDNA, which is critical for Pif1's activities. BaPif1 cocrystallized with a tailed dsDNA and ADP-AlF4(-), resulting in a bound ssDNA bent nearly 90° at the ssDNA/dsDNA junction. The conformational snapshots of BaPif1 provide insights into the mechanism governing the helicase activity of Pif1.

  16. 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

  17. Prebiotic galactooligosaccharides activate mucin and pectic galactan utilization pathways in the human gut symbiont Bacteroides thetaiotaomicron

    PubMed Central

    Lammerts van Bueren, Alicia; Mulder, Marieke; Leeuwen, Sander van; Dijkhuizen, Lubbert

    2017-01-01

    Galactooligosaccharides (GOS) are prebiotic carbohydrates that impart changes in the gut bacterial composition of formula-fed infants to more closely resemble that of breast-fed infants. Consuming human milk oligosaccharides (HMOs) provides specific bacterial strains with an advantage for colonizing the infant intestine. These same effects are seen in infants after GOS consumption, however GOS are very complex mixtures and the underlying molecular mechanisms of how GOS mimic HMOs are relatively unknown. Here we studied the effects of GOS utilization on a prominent gut symbiont, Bacteroides thetaiotaomicron, which has been previously shown to consume HMOs via mucin O-glycan degradation pathways. We show that several pathways for targeting O-mucin glycans are activated in B. thetaiotaomicron by GOS, as well as the galactan utilization sytem. Characterization of the endo-galactanase from this system identified activity on various longer GOS substrates while a subset of GOS compounds were identified as potential activators of mucin glycan metabolism in B. thetaiotaomicron. Our results show that GOS functions as an inducer of mucin-glycan pathways while providing a nutrient source in the form of β-(1 → 4)-galactan. These metabolic features of GOS mixtures may serve to explain the beneficial effects that are seen for GOS supplemented infant formula. PMID:28091546

  18. Structural analysis of arabinose-5-phosphate isomerase from Bacteroides fragilis and functional implications.

    PubMed

    Chiu, Hsiu Ju; Grant, Joanna C; Farr, Carol L; Jaroszewski, Lukasz; Knuth, Mark W; Miller, Mitchell D; Elsliger, Marc André; Deacon, Ashley M; Godzik, Adam; Lesley, Scott A; Wilson, Ian A

    2014-10-01

    The crystal structure of arabinose-5-phosphate isomerase (API) from Bacteroides fragilis (bfAPI) was determined at 1.7 Å resolution and was found to be a tetramer of a single-domain sugar isomerase (SIS) with an endogenous ligand, CMP-Kdo (cytidine 5'-monophosphate-3-deoxy-D-manno-oct-2-ulosonate), bound at the active site. API catalyzes the reversible isomerization of D-ribulose 5-phosphate to D-arabinose 5-phosphate in the first step of the Kdo biosynthetic pathway. Interestingly, the bound CMP-Kdo is neither the substrate nor the product of the reaction catalyzed by API, but corresponds to the end product in the Kdo biosynthetic pathway and presumably acts as a feedback inhibitor for bfAPI. The active site of each monomer is located in a surface cleft at the tetramer interface between three monomers and consists of His79 and His186 from two different adjacent monomers and a Ser/Thr-rich region, all of which are highly conserved across APIs. Structure and sequence analyses indicate that His79 and His186 may play important catalytic roles in the isomerization reaction. CMP-Kdo mimetics could therefore serve as potent and specific inhibitors of API and provide broad protection against many different bacterial infections.

  19. Structural analysis of arabinose-5-phosphate isomerase from Bacteroides fragilis and functional implications

    PubMed Central

    Chiu, Hsiu-Ju; Grant, Joanna C.; Farr, Carol L.; Jaroszewski, Lukasz; Knuth, Mark W.; Miller, Mitchell D.; Elsliger, Marc-André; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A.

    2014-01-01

    The crystal structure of arabinose-5-phosphate isomerase (API) from Bacteroides fragilis (bfAPI) was determined at 1.7 Å resolution and was found to be a tetramer of a single-domain sugar isomerase (SIS) with an endogenous ligand, CMP-Kdo (cytidine 5′-monophosphate-3-deoxy-d-manno-oct-2-ulosonate), bound at the active site. API catalyzes the reversible isomerization of d-ribulose 5-phosphate to d-arabinose 5-phosphate in the first step of the Kdo biosynthetic pathway. Interestingly, the bound CMP-Kdo is neither the substrate nor the product of the reaction catalyzed by API, but corresponds to the end product in the Kdo biosynthetic pathway and presumably acts as a feedback inhibitor for bfAPI. The active site of each monomer is located in a surface cleft at the tetramer interface between three monomers and consists of His79 and His186 from two different adjacent monomers and a Ser/Thr-rich region, all of which are highly conserved across APIs. Structure and sequence analyses indicate that His79 and His186 may play important catalytic roles in the isomerization reaction. CMP-Kdo mimetics could therefore serve as potent and specific inhibitors of API and provide broad protection against many different bacterial infections. PMID:25286848

  20. 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

  1. Oxygen-independent killing of Bacteroides fragilis by granule extracts from human polymorphonuclear leukocytes.

    PubMed Central

    Wetherall, B L; Pruul, H; McDonald, P J

    1984-01-01

    Granule proteins from human neutrophils were prepared by extraction with acetate, and their antibacterial activity against Bacteroides fragilis was determined. Activity was highly dependent on pH; greatest killing occurred at the most acid pH tested (pH 5.0). Optimum activity was observed at physiological ionic strength and low bacterial numbers. Killing was inhibited by incubation temperatures of less than 37 degrees C. Eight times more extract was required to kill 50% of stationary-phase bacteria, compared with those growing in logarithmic phase. The antibacterial effect of granule extract was destroyed by boiling, but some activity was retained after heating to 56 degrees C and 80 degrees C. Granule extract activity was tested under conditions in which oxygen-dependent antibacterial systems were inhibited. The rate and extent of killing was not affected by anaerobiosis, sodium azide, or cysteine hydrochloride. These results suggest that the activity of granule extract is independent of oxidative antibacterial systems, and therefore, under conditions that occur in anaerobic infections, potent leukocyte granule-associated mechanisms exist for the destruction of B. fragilis. PMID:6698601

  2. Inactivation of key factors of the plasma proteinase cascade systems by Bacteroides gingivalis.

    PubMed Central

    Nilsson, T; Carlsson, J; Sundqvist, G

    1985-01-01

    The effect of Bacteroides gingivalis W83 on various key components of the human plasma proteinase cascade systems was studied. When purified C1-inhibitor was incubated with the bacterium, the inhibitor was rapidly inactivated by limited proteolytic cleavage. In citrated whole plasma, C1-inhibitor, antithrombin, plasminogen, prekallikrein, prothrombinase complex, the clotting factor X, and most of the alpha 2-antiplasmin were functionally eliminated after 30 min of incubation with the bacterium. Fibrinogen disappeared from the plasma almost immediately upon mixing with the bacterial suspension. In contrast, there was no appreciable decrease in the bulk of other plasma proteins, such as various transport proteins (albumin, prealbumin, transferrin) and immunoglobulins, during 4 h of incubation with the bacterium. Most of the observed effects can be assigned to the proteolytic activity of the bacterium itself, since there was little evidence for generation of intrinsic plasma proteinase activity, despite the loss of proteinase inhibitory activities. B. gingivalis W83 thus seems to be equipped with proteolytic enzyme systems which selectively recognize and rapidly inactivate the most important proteinase inhibitors and proenzymes present in human plasma. This bacterium therefore seems to be able to efficiently paralyze the host's various defenses against invading microorganisms. Images PMID:3902645

  3. An Orthologue of Bacteroides fragilis NanH Is the Principal Sialidase in Tannerella forsythia▿

    PubMed Central

    Thompson, Hayley; Homer, Karen A.; Rao, Susmitha; Booth, Veronica; Hosie, Arthur H. F.

    2009-01-01

    Sialidase activity is a putative virulence factor of the anaerobic periodontal pathogen Tannerella forsythia, but it is uncertain which genes encode this activity. Characterization of a putative sialidase, SiaHI, by others, indicated that this protein alone may not be responsible for all of the sialidase activity. We describe a second sialidase in T. forsythia (TF0035), an orthologue of Bacteroides fragilis NanH, and its expression in Escherichia coli. Sialidase activity of the expressed NanH was confirmed by using 2′-(4-methylumbelliferyl)-α-d-N-acetylneuraminic acid as a substrate. Biochemical characterization of the recombinant T. forsythia NanH indicated that it was active over a broad pH range, with optimum activity at pH 5.5. This enzyme has high affinity for 2′-(4-methylumbelliferyl)-α-d-N-acetylneuraminic acid (Km of 32.9 ± 10.3 μM) and rapidly releases 4-methylumbelliferone (Vmax of 170.8 ± 11.8 nmol of 4-methylumbelliferone min−1 mg of protein−1). E. coli lysates containing recombinant T. forsythia NanH cleave sialic acid from a range of substrates, with a preference for α2-3 glycosidic linkages. The genes adjacent to nanH encode proteins apparently involved in the metabolism of sialic acid, indicating that the NanH sialidase is likely to be involved in nutrient acquisition. PMID:19304852

  4. An orthologue of Bacteroides fragilis NanH is the principal sialidase in Tannerella forsythia.

    PubMed

    Thompson, Hayley; Homer, Karen A; Rao, Susmitha; Booth, Veronica; Hosie, Arthur H F

    2009-06-01

    Sialidase activity is a putative virulence factor of the anaerobic periodontal pathogen Tannerella forsythia, but it is uncertain which genes encode this activity. Characterization of a putative sialidase, SiaHI, by others, indicated that this protein alone may not be responsible for all of the sialidase activity. We describe a second sialidase in T. forsythia (TF0035), an orthologue of Bacteroides fragilis NanH, and its expression in Escherichia coli. Sialidase activity of the expressed NanH was confirmed by using 2'-(4-methylumbelliferyl)-alpha-D-N-acetylneuraminic acid as a substrate. Biochemical characterization of the recombinant T. forsythia NanH indicated that it was active over a broad pH range, with optimum activity at pH 5.5. This enzyme has high affinity for 2'-(4-methylumbelliferyl)-alpha-D-N-acetylneuraminic acid (K(m) of 32.9 +/- 10.3 microM) and rapidly releases 4-methylumbelliferone (V(max) of 170.8 +/- 11.8 nmol of 4-methylumbelliferone min(-1) mg of protein(-1)). E. coli lysates containing recombinant T. forsythia NanH cleave sialic acid from a range of substrates, with a preference for alpha2-3 glycosidic linkages. The genes adjacent to nanH encode proteins apparently involved in the metabolism of sialic acid, indicating that the NanH sialidase is likely to be involved in nutrient acquisition.

  5. 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

  6. The enigma of non-gonococcal urethritis: role for Bacteroides ureolyticus.

    PubMed Central

    Hawkins, D A; Fontaine, E A; Thomas, B J; Boustouller, Y L; Taylor-Robinson, D

    1988-01-01

    Although up to about half the cases of acute non-gonococcal urethritis (NGU) are caused by Chlamydia trachomatis organisms (chlamydiae) and a smaller, ill-defined, proportion probably by Ureaplasma urealyticum organisms (ureaplasmas), the aetiology of all cases is not understood. Clarification of the role of the anaerobe, Bacteroides ureolyticus, was sought in the current study. Seventy five chlamydia negative patients with NGU were treated on a double blind placebo controlled basis with metronidazole. After seven days more of the 35 patients given this drug tended to improve clinically than the 40 given the placebo, but the difference was not significant. Of 23 chlamydia negative but anaerobe positive men, however, 78% (7/9) receiving metronidazole responded clinically, but only 7% (1/14) receiving placebo responded (p less than 0.001). Furthermore, whereas 78% of the anaerobe positive men given metronidazole recovered, only 23% (6/26) of the anaerobe negative men did so (p less than 0.02). No further evidence for the role of ureaplasmas in the aetiology of NGU was obtained, but the data suggest that B ureolyticus organisms, and perhaps other anaerobes, have an important role in a small proportion of cases and that the beneficial effects of metronidazole given on an empirical basis will be confined to anaerobe positive urethritis. PMID:3278969

  7. Gut commensal Bacteroides acidifaciens prevents obesity and improves insulin sensitivity in mice.

    PubMed

    Yang, J-Y; Lee, Y-S; Kim, Y; Lee, S-H; Ryu, S; Fukuda, S; Hase, K; Yang, C-S; Lim, H S; Kim, M-S; Kim, H-M; Ahn, S-H; Kwon, B-E; Ko, H-J; Kweon, M-N

    2017-01-01

    In humans, the composition of gut commensal bacteria is closely correlated with obesity. The bacteria modulate metabolites and influence host immunity. In this study, we attempted to determine whether there is a direct correlation between specific commensal bacteria and host metabolism. As mice aged, we found significantly reduced body weight and fat mass in Atg7(ΔCD11c) mice when compared with Atg7(f/f) mice. When mice shared commensal bacteria by co-housing or feces transfer experiments, body weight and fat mass were similar in both mouse groups. By pyrosequencing analysis, Bacteroides acidifaciens (BA) was significantly increased in feces of Atg7(ΔCD11c) mice compared with those of control Atg7(f/f) mice. Wild-type C57BL/6 (B6) mice fed with BA were significantly more likely to gain less weight and fat mass than mice fed with PBS. Of note, the expression level of peroxisome proliferator-activated receptor alpha (PPARα) was consistently increased in the adipose tissues of Atg7(ΔCD11c) mice, B6 mice transferred with fecal microbiota of Atg7(ΔCD11c) mice, and BA-fed B6 mice. Furthermore, B6 mice fed with BA showed elevated insulin levels in serum, accompanied by increased serum glucagon-like peptide-1 and decreased intestinal dipeptidyl peptidase-4. These finding suggest that BA may have potential for treatment of metabolic diseases such as diabetes and obesity.

  8. Succinic acid production from Bacteroides fragilis: process optimization and scale up in a bioreactor.

    PubMed

    Isar, Jasmine; Agarwal, Lata; Saran, Saurabh; Saxena, Rajendra Kumar

    2006-01-01

    We report the effect of different physiological and nutritional parameters on succinic acid production from Bacteroides fragilis. This strain initially produced 0.70gL(-1) of succinic acid in 60h. However, when process optimization was employed, 5.4gL(-1) of succinic acid was produced in medium consisting of glucose (1.5%); tryptone (2.5%); Na(2)CO(3) (1.5%), at pH 7.0, when inoculated with 4% inoculum and incubated at 37 degrees C, 100rpm for 48h. A marked enhancement in succinic acid production was observed when the optimized conditions were employed in a 10L bioreactor. A total of 12.5gL(-1) of succinic acid was produced in 30h. This is approximately 12-fold increase in succinic acid production when compared to the initial un-optimized medium production. This enhancement in succinic acid production may be due to the control of CO(2) supply and the impeller speed. This is also resulted in the reduction of the production time. The present study provides useful information to the industrialists seeking environmentally benign technology for the production of bulk biomolecules through manipulation of various chemical parameters.

  9. Occurrence of enterotoxigenic and nonenterotoxigenic Bacteroides fragilis in calves and evaluation of their antimicrobial susceptibility.

    PubMed

    Almeida, Fernanda S; Nakano, Viviane; Avila-Campos, Mario J

    2007-07-01

    Bacteroides fragilis is considered an important clinical pathogen and the most common anaerobe isolated from human and animal clinical specimens; enterotoxigenic strains produce diarrhea. The presence of enterotoxigenic (ETBF) and nonenterotoxigenic B. fragilis in stool samples from calves with or without acute diarrhea and the antimicrobial susceptibility of the strains were evaluated. The stool samples were plated onto a selective B. fragilis-bile-esculin agar, and incubated anaerobically (10% CO(2)/90% N(2)), at 37 degrees C, for 72 h. Species of the B. fragilis group were identified by using the API 32-A kit. Enterotoxigenic strains were detected by PCR and the cytotoxic assay. From 54 diarrhea and 54 nondiarrhea stools, 124 and 92 members of the B. fragilis group, respectively, were recovered. Only two ETBF strains were isolated from two different diarrhea samples and the bft gene was detected in both. Moreover, the bft gene was detected in DNA from four different diarrheal stools samples but no ETBF strain was recovered. All the bacteria were susceptible to chloramphenicol, imipenem, moxifloxacin, piperacillin/tazobactam, metronidazole and tigecycline. Most of the isolates from both calves with and without diarrhea were resistant to all metals. Our results are of concern, and suggest the need to increase the surveillance of antibiotic and metal resistance of this microbial group isolated from animal production such as calves.

  10. 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.

  11. 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

  12. Regulation of Product Formation in Bacteroides xylanolyticus X5-1 by Interspecies Electron Transfer

    PubMed Central

    Biesterveld, Steven; Zehnder, Alexander J. B.; Stams, Alfons J. M.

    1994-01-01

    Bacteroides xylanolyticus X5-1 was grown in pure culture and in mixed culture with Methanospirillum hungatei JF-1 under xylose limitation in the chemostat. In the pure culture, ethanol, acetate, CO2, and hydrogen were the products. In the mixed culture, acetate, CO2, and presumably hydrogen were the only products formed by B. xylanolyticus X5-1. The biomass yield of B. xylanolyticus X5-1 increased because of cocultivation. In cell extracts of the pure culture, both NAD- and NADP-dependent acetaldehyde dehydrogenase and ethanol dehydrogenase activities were found. In cell extracts of the mixed culture, activities of these enzymes were not detected. Inhibition of methanogenesis in the mixed culture by the addition of bromoethanosulfonic acid (BES) resulted in an accumulation of H2, ethanol, and formate. Immediately after the addition of BES, NAD-dependent acetaldehyde dehydrogenase and ethanol dehydrogenase activities were detected. After a short lag phase, a NADP-dependent ethanol dehydrogenase was also detectable. The induction of acetaldehyde dehydrogenase and ethanol dehydrogenase was inhibited by chloramphenicol, suggesting de novo synthesis of these enzymes. These results are consistent with a model in which the shift in product formation caused by interspecies electron transfer is regulated at the level of enzyme synthesis. PMID:16349240

  13. 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)).

  14. 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)).

  15. Rhizobium alkalisoli sp. nov., isolated from Caragana intermedia growing in saline-alkaline soils in the north of China.

    PubMed

    Li Lu, Yang; Chen, Wen Feng; Li Han, Li; Wang, En Tao; Chen, Wen Xin

    2009-12-01

    Three rhizobial strains (CCBAU 01393(T), CCBAU 01389 and CCBAU 03239) isolated from nodules of Caragana intermedia grown in saline-alkaline soils in the north of China had identical 16S rRNA genes that showed 99.7 and 99.5 % sequence similarities with those of Rhizobium huautlense SO2(T) and Rhizobium galegae USDA 4128(T), respectively. Phylogenies of the housekeeping genes atpD, recA and glnII confirmed their distinct position, differing from recognized Rhizobium species. SDS-PAGE of whole-cell soluble proteins and a series of phenotypic and physiological tests allowed us to differentiate the novel group from all closely related recognized Rhizobium species. The levels of DNA-DNA relatedness between strain CCBAU 01393(T) and R. huautlense SO2(T) and R. galegae USDA 4128(T) were 34.9 and 20.5 %, respectively. Therefore, we propose that strains CCBAU 01393(T), CCBAU 01389 and CCBAU 03239 represent a novel species, Rhizobium alkalisoli sp. nov., with strain CCBAU 01393(T) (=LMG 24763(T)=HAMBI 3051(T)) as the type strain. This strain could form effective nodules on Caragana microphylla, Phaseolus vulgaris and Vigna radiata.

  16. Classification of Austrian rhizobia and the Mexican isolate FL27 obtained from Phaseolus vulgaris L. as Rhizobium gallicum.

    PubMed

    Sessitsch, A; Ramírez-Saad, H; Hardarson, G; Akkermans, A D; de Vos, W M

    1997-10-01

    The phylogenetic positions of four rhizobial strains obtained from nodules of common bean plants (Phaseolus vulgaris L.) grown in an Austrian soil and of the Mexican bean isolate FL27 are described. Analysis of the 16S rRNA genes revealed sequences almost identical to that of the Rhizobium gallicum type strain, R602sp, with a maximum of two nucleotide substitutions. Comparison of the 16S rRNA gene sequences with those from other bacteria indicated highest similarity to Rhizobium sp. strain OK-50, Rhizobium leguminosarum IAM 12609, and Rhizobium etli. DNA homology determined by DNA-DNA hybridization was high among the Austrian isolates and R602spT (45 to 90%) and ranged from 21 to 65% with FL27, but hybridization analysis revealed very low homology to the recognized common bean-nodulating species, R. leguminosarum bv. phaseoli, R. etli, and Rhizobium tropici. Ribosomal gene organization was studied by Southern hybridization with the 16S rRNA gene and temperature gradient gel electrophoresis, indicating identical organizations and the presence of three identical 16S rRNA copies in the genome of this species. The six strains investigated showed different plasmid profiles based on their geographical origins. We propose that the Austrian isolates and the Mexican strain FL27 are members of the species R. gallicum.

  17. Transgenic Leucaena leucocephala expressing the Rhizobium gene pydA encoding a meta-cleavage dioxygenase shows reduced mimosine content.

    PubMed

    Jube, Sandro L R; Borthakur, Dulal

    2010-04-01

    The use of the tree-legume Leucaena leucocephala (leucaena), which contains high levels of proteins in its foliage, is limited due to the presence of the toxic free amino acid mimosine. The goal of this research was to develop transgenic leucaena with reduced mimosine content. Two genes, pydA and pydB, encoding a meta-cleavage dioxygenase (EC 1.13.11.2) and a pyruvate hydrolase (EC 3.7.1.6), respectively, from the mimosine-degrading leucaena symbiont Rhizobium sp. strain TAL1145, were used to transform leucaena. These bacterial genes were sequence-optimized for expression in leucaena and cloned into the plant binary vector pCAMBIA3201 for Agrobacterium tumefaciens-mediated transformation. Using immature zygotic embryos as the start explant material, six pydA and three pydB transgenic lines were developed. The presence and expression of the bacterial genes in the transgenic lines were verified by PCR, reverse transcriptase PCR, and Southern analyses. HPLC analyses of the transgenic plants determined that the mimosine contents of the pydA-expressing lines were reduced up to 22.5% in comparison to the wild-type. No significant reduction in mimosine content was observed in the pydB-expressing lines. This is the first example of using a gene from a bacterial symbiont to reduce the toxicity of a tree-legume.

  18. 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.

  19. Chemical characterization and biologic properties of lipopolysaccharide from Bacteroides gingivalis strains W50, W83, and ATCC 33277.

    PubMed

    Bramanti, T E; Wong, G G; Weintraub, S T; Holt, S C

    1989-12-01

    The chemistry and selected biological activity of lipopolysaccharide (LPS) from Bacteroides gingivalis strains W50, W83, and ATCC 33277 were compared, as well as the role of this molecule as a mediator of selected inflammatory responses. Chemically, the LPSs consisted of 47-58% Lipid A, 5-10% carbohydrate, 0.05% 3-deoxy 2-octulosonic acid, 0.3% heptose, 3.8-5.2% hexosamine, and 2% phosphate. Rhamnose represented the dominant sugar (26-36%), with lesser amounts of glucose (18-34%), galactose (18-25%), mannose (9-12%), glucosamine (7-11%), and galactosamine (2-5%). The major fatty acids were: 13-methyl-tetradecanoate (42-45%), 3-OH-heptadecanoate (21-23%), hexadecanoate (16-19%), and 12-methyl-tetradecanoate (6-8%). SDS-PAGE and sodium deoxycholate-PAGE revealed the LPS to be a smooth chemotype. Differences in migration patterns between the virulent and avirulent strain LPSs also occurred. C3H/HeN macrophages (Mø) exposed to 1 microgram/ml of LPS released 3.2-4.2 ng of prostaglandin E (PGE)/ml of supernatant, representing 236-278% of control. Interleukin-1 (IL-1) activity in C3H/HeN and C3H/HeJ Mø exposed to 50 micrograms of LPS/ml was 382-724% and 270-300% of control, respectively; similar Mø exposed to 10 micrograms of LPS/ml released 1.6-2.0 ng and 0.3-0.5 ng of tumor necrosis factor (TNF)/ml of supernatant, respectively. Maximum TNF release in C3H/HeN Mø occurred in response to 50 micrograms of LPS/ml, and was sustained for up to 96 hours. These results suggest that LPS from the B. gingivalis strains stimulate cytokine production from Mø which, in turn, may play a role in orchestrating the inflammatory response for the development of periodontal diseases.

  20. 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.

  1. 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

  2. The influence of the long chain fatty acid on the antagonistic activities of Rhizobium sin-1 lipid A

    PubMed Central

    Zhang, Yanghui; Wolfert, Margreet A.; Boons, Geert-Jan

    2007-01-01

    The lipid A from nitrogen-fixing bacterial species R. sin-1 is structurally unusual due to lack of phosphates and the presence of a 2-aminogluconolactone and a very long chain fatty acid, 27-hydroxyoctacosanoic acid (27OHC28:0), moiety. This structurally unusual lipid A can antagonize TNF-α production by human monocytes induced by E. coli LPS. To establish the relevance of the unusual long chain 27-hydroxyoctacosanoic acid for antagonistic properties, a highly convergent strategy for the synthesis of several derivatives of the lipid A of Rhizobium sin-1 has been developed. Compound 1 is a natural R. sin-1 lipid A having a 27-hydroxyoctacosanoic acid at C-2′, compound 2 contains an octacosanoic acid moiety at this position, and compound 3 is modified by a short chain tetradecanoic acid. Cellular activation studies with a human monocytic cell line have shown that the octacosanoic acid is important for optimal antagonistic properties. The hydroxyl of the natural 27-hydroxyoctacosanoic moiety does, however, not account for inhibitory activity. The resulting structure activity relationships are important for the design of compounds for the treatment of septic shock. PMID:17513113

  3. A previously uncharacterized tetratricopeptide-repeat-containing protein is involved in cell envelope function in Rhizobium leguminosarum.

    PubMed

    Neudorf, Kara D; Vanderlinde, Elizabeth M; Tambalo, Dinah D; Yost, Christopher K

    2015-01-01

    Rhizobium leguminosarum is a soil bacterium that is an intracellular symbiont of leguminous plants through the formation of nitrogen-fixing root nodules. Due to the changing environments that rhizobia encounter, the cell is often faced with a variety of cell altering stressors that can compromise the cell envelope integrity. A previously uncharacterized operon (RL3499-RL3502) has been linked to proper cell envelope function, and mutants display pleiotropic phenotypes including an inability to grow on peptide-rich media. In order to identify functional partners to the operon, suppressor mutants capable of growth on complex, peptide-rich media were isolated. A suppressor mutant of a non-polar mutation to RL3500 was chosen for further characterization. Transposon mutagenesis, screening for loss of the suppressor phenotype, led to the identification of a Tn5 insertion in an uncharacterized tetratricopeptide-repeat-containing protein RL0936. Furthermore, RL0936 had a 3.5-fold increase in gene expression in the suppressor strain when compared with the WT and a 1.5-fold increase in the original RL3500 mutant. Mutation of RL0936 decreased desiccation tolerance and lowered the ability to form biofilms when compared with the WT strain. This work has identified a potential interaction between RL0936 and the RL3499-RL3502 operon that is involved in cell envelope development in R. leguminosarum, and has described phenotypic activities to a previously uncharacterized conserved hypothetical gene.

  4. Relevance of fucose-rich extracellular polysaccharides produced by Rhizobium sullae strains nodulating Hedysarum coronarium l. legumes.

    PubMed

    Gharzouli, Razika; Carpéné, Marie-Anne; Couderc, François; Benguedouar, Ammar; Poinsot, Véréna

    2013-03-01

    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.

  5. 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

  6. Theoretical and Experimental Characterization of the Scope of Protein O-Glycosylation in Bacteroides fragilis*

    PubMed Central

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

    2011-01-01

    Among bacterial species demonstrated to have protein O-glycosylation systems, that of Bacteroides fragilis and related species is unique in that extracytoplasmic proteins are glycosylated at serine or threonine residues within the specific three-amino acid motif D(S/T)(A/I/L/M/T/V). This feature allows for computational analysis of the proteome to identify candidate glycoproteins. With the criteria of a signal peptidase I or II cleavage site or a predicted transmembrane-spanning region and the presence of at least one glycosylation motif, we identified 1021 candidate glycoproteins of B. fragilis. In addition to the eight glycoproteins identified previously, we confirmed that another 12 candidate glycoproteins are in fact glycosylated. These included four glycoproteins that are predicted to localize to the inner membrane, a compartment not previously shown to include glycosylated proteins. In addition, we show that four proteins involved in cell division and chromosomal segregation, two of which are encoded by candidate essential genes, are glycosylated. To date, we have not identified any extracytoplasmic proteins containing a glycosylation motif that are not glycosylated. Therefore, based on the list of 1021 candidate glycoproteins, it is likely that hundreds of proteins, comprising more than half of the extracytoplasmic proteins of B. fragilis, are glycosylated. Site-directed mutagenesis of several glycoproteins demonstrated that all are glycosylated at the identified glycosylation motif. By engineering glycosylation motifs into a naturally unglycosylated protein, we are able to bring about site-specific glycosylation at the engineered sites, suggesting that this glycosylation system may have applications for glycoengineering. PMID:21115495

  7. Azide protection of bacteroides superoxide dismutases from inactivation by hydrogen peroxide

    SciTech Connect

    Barkley, K.B.; Gregory, E.M.

    1986-05-01

    The anaerobes Bacteroides fragilis, B. distasonis and B. thetaiotaomicron produce an iron-containing superoxide dismutase (FeSOD). These FeSODs are reversibly inhibited by 1 mM azide (NaN/sub 3/) and are irreversibly inactivated upon incubation with hydrogen peroxide (H/sub 2/O/sub 2/). H/sub 2/O/sub 2/ inactivation of the enzyme likely depends on a Fenton type reaction with the production of hydroxyl radical (OH). Addition of NaN/sub 3/ to the enzyme solution decreased the rate of inactivation by H/sub 2/O/sub 2/. After 20 minutes incubation of purified B. distasonis FeSOD with 2.5 mM H/sub 2/O/sub 2/, 61% of the initial enzymatic activity remained when 1 mM NaN/sub 3/ was also present compared with 29% activity without NaN/sub 3/. Similar results were seen with FeSOD from B. fragilis and B. thetaiotaomicron. Metal analyses of the native, peroxidized, and NaN/sub 3/ protected samples are consistent with loss of Fe from the enzyme upon peroxidation, but retention of Fe and enzymatic activity in the NaN/sub 3/ protected sample. Protection of FeSOD activity from H/sub 2/O/sub 2/ inactivation was dependent on NaN/sub 3/ concentration. Anionic hydroxyl radical scavengers, such as urate and xanthine did not significantly protect the enzyme. The results are consistent with binding of azide to the active site either preventing entry of H/sub 2/O/sub 2/ or altering Fe redox potential, preventing OH production.

  8. Exploratory Investigation of Bacteroides fragilis Transcriptional Response during In vitro Exposure to Subinhibitory Concentration of Metronidazole

    PubMed Central

    de Freitas, Michele C. R.; Resende, Juliana A.; Ferreira-Machado, Alessandra B.; Saji, Guadalupe D. R. Q.; de Vasconcelos, Ana T. R.; da Silva, Vânia L.; Nicolás, Marisa F.; Diniz, Cláudio G.

    2016-01-01

    Bacteroides fragilis, member from commensal gut microbiota, is an important pathogen associated to endogenous infections and metronidazole remains a valuable antibiotic for the treatment of these infections, although bacterial resistance is widely reported. Considering the need of a better understanding on the global mechanisms by which B. fragilis survive upon metronidazole exposure, we performed a RNA-seq transcriptomic approach with validation of gene expression results by qPCR. Bacteria strains were selected after in vitro subcultures with subinhibitory concentration (SIC) of the drug. From a wild type B. fragilis ATCC 43859 four derivative strains were selected: first and fourth subcultures under metronidazole exposure and first and fourth subcultures after drug removal. According to global gene expression analysis, 2,146 protein coding genes were identified, of which a total of 1,618 (77%) were assigned to a Gene Ontology term (GO), indicating that most known cellular functions were taken. Among these 2,146 protein coding genes, 377 were shared among all strains, suggesting that they are critical for B. fragilis survival. In order to identify distinct expression patterns, we also performed a K-means clustering analysis set to 15 groups. This analysis allowed us to detect the major activated or repressed genes encoding for enzymes which act in several metabolic pathways involved in metronidazole response such as drug activation, defense mechanisms against superoxide ions, high expression level of multidrug efflux pumps, and DNA repair. The strains collected after metronidazole removal were functionally more similar to those cultured under drug pressure, reinforcing that drug-exposure lead to drastic persistent changes in the B. fragilis gene expression patterns. These results may help to elucidate B. fragilis response during metronidazole exposure, mainly at SIC, contributing with information about bacterial survival strategies under stress conditions in their

  9. 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.

  10. l-Galactose metabolism in Bacteroides vulgatus from the human gut microbiota.

    PubMed

    Hobbs, Merlin Eric; Williams, Howard J; Hillerich, Brandan; Almo, Steven C; Raushel, Frank M

    2014-07-22

    A previously unknown metabolic pathway for the utilization of l-galactose was discovered in a prevalent gut bacterium, Bacteroides vulgatus. The new pathway consists of three previously uncharacterized enzymes that were found to be responsible for the conversion of l-galactose to d-tagaturonate. Bvu0219 (l-galactose dehydrogenase) was determined to oxidize l-galactose to l-galactono-1,5-lactone with kcat and kcat/Km values of 21 s(-1) and 2.0 × 10(5) M(-1) s(-1), respectively. The kinetic product of Bvu0219 is rapidly converted nonenzymatically to the thermodynamically more stable l-galactono-1,4-lactone. Bvu0220 (l-galactono-1,5-lactonase) hydrolyzes both the kinetic and thermodynamic products of Bvu0219 to l-galactonate. However, l-galactono-1,5-lactone is estimated to be hydrolyzed 300-fold faster than its thermodynamically more stable counterpart, l-galactono-1,4-lactone. In the final step of this pathway, Bvu0222 (l-galactonate dehydrogenase) oxidizes l-galactonate to d-tagaturonate with kcat and kcat/Km values of 0.6 s(-1) and 1.7 × 10(4) M(-1) s(-1), respectively. In the reverse direction, d-tagaturonate is reduced to l-galactonate with values of kcat and kcat/Km of 90 s(-1) and 1.6 × 10(5) M(-1) s(-1), respectively. d-Tagaturonate is subsequently converted to d-glyceraldehyde and pyruvate through enzymes encoded within the degradation pathway for d-glucuronate and d-galacturonate.

  11. 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

  12. Evidence that Porphyromonas (Bacteroides) gingivalis fimbriae function in adhesion to Actinomyces viscosus.

    PubMed Central

    Goulbourne, P A; Ellen, R P

    1991-01-01

    Porphyromonas (Bacteroides) gingivalis adheres to gram-positive bacteria, such as Actinomyces viscosus, when colonizing the tooth surface. However, little is known of the adhesins responsible for this interaction. A series of experiments were performed to determine whether P. gingivalis fimbriae function in its coadhesion with A. viscosus. Fimbriae typical of P. gingivalis were isolated from strain 2561 (ATCC 33277) by the method of Yoshimura et al. (F. Yoshimura, K. Takahashi, Y. Nodasaka, and T. Suzuki, J. Bacteriol. 160:949-957, 1984) in fractions enriched with a 40-kDa subunit, the fimbrillin monomer, P. gingivalis-A. viscosus coaggregation was inhibited by purified rabbit antifimbrial immunoglobulin G (IgG) at dilutions eightfold higher than those of preimmune IgG, providing indirect evidence implicating P. gingivalis fimbriae in coadhesion. Three types of direct binding assays further supported this observation. (i) Mixtures of isolated P. gingivalis fimbriae and A. viscosus WVU627 cells were incubated for 1 h, washed vigorously with phosphate-buffered saline (pH 7.2), and subjected to electrophoresis. Transblots onto nitrocellulose were probed with antifimbrial antiserum. Fimbrillin labeled positively on these blots. No reaction occurred with the control protein, porcine serum albumin, when blots were exposed to anti-porcine serum albumin, (ii) A. viscosus cells incubated with P. gingivalis fimbriae were agglutinated only after the addition of antifimbrial antibodies. (iii) Binding curves generated from an enzyme immunoassay demonstrated concentration-dependent binding of P. gingivalis fimbriae to A. viscosus cells. From these lines of evidence, P. gingivalis fimbriae appear to be capable of binding to A. viscosus and mediating the coadhesion of these species. Images PMID:1679428

  13. Adhesion of Actinomyces viscosus to Porphyromonas (Bacteroides) gingivalis-coated hexadecane droplets.

    PubMed Central

    Rosenberg, M; Buivids, I A; Ellen, R P

    1991-01-01

    Interbacterial adhesion (coadhesion) is considered a major determinant of dental plaque ecology. In this report, we studied several aspects of the adhesion of Porphyromonas (Bacteroides) gingivalis to hexadecane in order to use the liquid hydrocarbon as a convenient substratum for coadhesion assays. Washed suspensions of hydrophobic P. gingivalis 2561 cells were vortexed with hexadecane to yield highly stable cell-coated droplets. Kinetics of coadhesion between Actinomyces viscosus cells and P. gingivalis-coated hexadecane droplets (PCHD) was subsequently studied. Aliquots of PCHD were added to A. viscosus suspensions, and the mixtures were gently rotated. Avid adhesion of A. viscosus cells to the immobilized P. gingivalis layer could be readily measured by the decrease in turbidity in the aqueous phase, following phase separation. Despite the ability of A. viscosus cells to adsorb to hexadecane following vigorous mixing, gentle mixing did not appreciably promote adhesion to bare hexadecane. Moreover, extensive microscopic examinations revealed that A. viscosus cells adhered exclusively to the bound P. gingivalis cells rather than to exposed areas of hexadecane. Coadhesion of A. viscosus to the PCHD appeared to follow first-order kinetics, attaining 80% levels within 30 min. Electron micrographs revealed A. viscosus cells adhering to the P. gingivalis cell layer adsorbed at the hexadecane-water interface. Interestingly, P. gingivalis cells did not appear to penetrate the hexadecane. A viscosus mutants lacking type 1 or type 2 fimbriae or both were still able to bind to the PCHD. No obvious correlation was observed between relative hydrophobicity of A. viscosus strains and their binding to PCHD. However, defatted bovine serum albumin, an inhibitor of hydrophobic interactions, was the most potent inhibitor among those tested. The data suggest that this approach provides a simple, quantitative technique for studying kinetics of bacterial coadhesion which is amenable

  14. Exploratory Investigation of Bacteroides fragilis Transcriptional Response during In vitro Exposure to Subinhibitory Concentration of Metronidazole.

    PubMed

    de Freitas, Michele C R; Resende, Juliana A; Ferreira-Machado, Alessandra B; Saji, Guadalupe D R Q; de Vasconcelos, Ana T R; da Silva, Vânia L; Nicolás, Marisa F; Diniz, Cláudio G

    2016-01-01

    Bacteroides fragilis, member from commensal gut microbiota, is an important pathogen associated to endogenous infections and metronidazole remains a valuable antibiotic for the treatment of these infections, although bacterial resistance is widely reported. Considering the need of a better understanding on the global mechanisms by which B. fragilis survive upon metronidazole exposure, we performed a RNA-seq transcriptomic approach with validation of gene expression results by qPCR. Bacteria strains were selected after in vitro subcultures with subinhibitory concentration (SIC) of the drug. From a wild type B. fragilis ATCC 43859 four derivative strains were selected: first and fourth subcultures under metronidazole exposure and first and fourth subcultures after drug removal. According to global gene expression analysis, 2,146 protein coding genes were identified, of which a total of 1,618 (77%) were assigned to a Gene Ontology term (GO), indicating that most known cellular functions were taken. Among these 2,146 protein coding genes, 377 were shared among all strains, suggesting that they are critical for B. fragilis survival. In order to identify distinct expression patterns, we also performed a K-means clustering analysis set to 15 groups. This analysis allowed us to detect the major activated or repressed genes encoding for enzymes which act in several metabolic pathways involved in metronidazole response such as drug activation, defense mechanisms against superoxide ions, high expression level of multidrug efflux pumps, and DNA repair. The strains collected after metronidazole removal were functionally more similar to those cultured under drug pressure, reinforcing that drug-exposure lead to drastic persistent changes in the B. fragilis gene expression patterns. These results may help to elucidate B. fragilis response during metronidazole exposure, mainly at SIC, contributing with information about bacterial survival strategies under stress conditions in their

  15. Susceptibility trends of Bacteroides fragilis group isolates from Buenos Aires, Argentina.

    PubMed

    Fernández Canigia, L; Castello, L; Di Martino, A; Greco, G; Legaria, M C; Litterio, M; Predari, S C; Rollet, R; Rossetti, A; Carloni, G; Sarchi, M I; Bianchini, H

    2007-01-01

    The aim of this study was to analyze the susceptibility trends to seven antibiotics of Bacteroides fragilis group isolates based on three survey studies performed by the Committee of Anaerobic Bacteria between 1989 and 2002. Fifty three, 82 and 65 B. fragilis group isolates were collected during each period. The antimicrobial agents included were: ampicillin, ampicillin-sulbactam (2:1), cefoxitin, piperacillin, imipenem, clindamycin, and metronidazole. Minimal inhibitory concentrations (MICs) were determined according to the reference agar dilution method described by the Clinical and Laboratory Standards Institute (CLSI, formerly NCCLS). The most active antibiotics for B. fragilis and non-B. fragilis species throughout the three periods were: imipenem with 99.1 and 100% of activity, respectively, and metronidazole with 100% of activity. The susceptibility to ampicillin-sulbactam showed a decrease, from 100% to 90.3% and to 82.4 % in the last period, for both B. fragilis and non-B. fragilis species, respectively. The overall susceptibility rates for cefoxitin, piperacillin, and clindamycin were significantly different between B. fragilis and non-B. fragilis species (84.2% vs. 56.5%; 85.9% vs. 66.7% and 88.8% vs. 64.7%, respectively, p < 0.05). Cefoxitin was the antibiotic that showed more variations as regards periods and species. The susceptibility rates for clindamycin were low, about 60%, for non-B. fragilis species during the last two periods. The variations observed in the susceptibility patterns of the B. fragilis group isolates emphasize the need to continue monitoring the emergence of resistance in order to guide the election of the most appropriate antibiotic therapy scheme for anaerobic infections.

  16. Bacteroides fragilis Lipopolysaccharide and Inflammatory Signaling in Alzheimer’s Disease

    PubMed Central

    Lukiw, Walter J.

    2016-01-01

    The human microbiome consists of ~3.8 × 1013 symbiotic microorganisms that form a highly complex and dynamic ecosystem: the gastrointestinal (GI) tract constitutes the largest repository of the human microbiome by far, and its impact on human neurological health and disease is becoming increasingly appreciated. Bacteroidetes, the largest phylum of Gram-negative bacteria in the GI tract microbiome, while generally beneficial to the host when confined to the GI tract, have potential to secrete a remarkably complex array of pro-inflammatory neurotoxins that include surface lipopolysaccharides (LPSs) and toxic proteolytic peptides. The deleterious effects of these bacterial exudates appear to become more important as GI tract and blood-brain barriers alter or increase their permeability with aging and disease. For example, presence of the unique LPSs of the abundant Bacteroidetes species Bacteroides fragilis (BF-LPS) in the serum represents a major contributing factor to systemic inflammation. BF-LPS is further recognized by TLR2, TLR4, and/or CD14 microglial cell receptors as are the pro-inflammatory 42 amino acid amyloid-beta (Aβ42) peptides that characterize Alzheimer’s disease (AD) brain. Here we provide the first evidence that BF-LPS exposure to human primary brain cells is an exceptionally potent inducer of the pro-inflammatory transcription factor NF-kB (p50/p65) complex, a known trigger in the expression of pathogenic pathways involved in inflammatory neurodegeneration. This ‘Perspectives communication’ will in addition highlight work from recent studies that advance novel and emerging concepts on the potential contribution of microbiome-generated factors, such as BF-LPS, in driving pro-inflammatory degenerative neuropathology in the AD brain. PMID:27725817

  17. 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.

  18. Erosion of root epidermal cell walls by Rhizobium polysaccharide-degrading enzymes as related to primary host infection in the Rhizobium-legume symbiosis.

    PubMed

    Mateos, P F; Baker, D L; Petersen, M; Velázquez, E; Jiménez-Zurdo, J I; Martínez-Molina, E; Squartini, A; Orgambide, G; Hubbell, D H; Dazzo, F B

    2001-06-01

    A central event of the infection process in the Rhizobium-legume symbiosis is the modification of the host cell wall barrier to form a portal of entry large enough for bacterial penetration. Transmission electron microscopy (TEM) indicates that rhizobia enter the legume root hair through a completely eroded hole that is slightly larger than the bacterial cell and is presumably created by localized enzymatic hydrolysis of the host cell wall. In this study, we have used microscopy and enzymology to further clarify how rhizobia modify root epidermal cell walls to shed new light on the mechanism of primary host infection in the Rhizobium-legume symbiosis. Quantitative scanning electron microscopy indicated that the incidence of highly localized, partially eroded pits on legume root epidermal walls that follow the contour of the rhizobial cell was higher in host than in nonhost legume combinations, was inhibited by high nitrate supply, and was not induced by immobilized wild-type chitolipooligosaccharide Nod factors reversibly adsorbed to latex beads. TEM examination of these partially eroded, epidermal pits indicated that the amorphous, noncrystalline portions of the wall were disrupted, whereas the crystalline portions remained ultrastructurally intact. Further studies using phase-contrast and polarized light microscopy indicated that (i) the structural integrity of clover root hair walls is dependent on wall polymers that are valid substrates for cell-bound polysaccharide-degrading enzymes from rhizobia, (ii) the major site where these rhizobial enzymes can completely erode the root hair wall is highly localized at the isotropic, noncrystalline apex of the root hair tip, and (iii) the degradability of clover root hair walls by rhizobial polysaccharide-degrading enzymes is enhanced by modifications induced during growth in the presence of chitolipooligosaccharide Nod factors from wild-type clover rhizobia. The results suggest a complementary role of rhizobial cell

  19. Rhizobium etli and Rhizobium gallicum Nodulate Common Bean (Phaseolus vulgaris) in a Traditionally Managed Milpa Plot in Mexico: Population Genetics and Biogeographic Implications

    PubMed Central

    Silva, Claudia; Vinuesa, Pablo; Eguiarte, Luis E.; Martínez-Romero, Esperanza; Souza, Valeria

    2003-01-01

    The stability of the genetic structure of rhizobial populations nodulating Phaseolus vulgaris cultivated in a traditionally managed milpa plot in Mexico was studied over three consecutive years. The set of molecular markers analyzed (including partial rrs, glnII, nifH, and nodB sequences), along with host range experiments, placed the isolates examined in Rhizobium etli bv. phaseoli and Rhizobium gallicum bv. gallicum. Cluster analysis of multilocus enzyme electrophoresis and plasmid profile data separated the two species and identified numerically dominant clones within each of them. Population genetic analyses showed that there was high genetic differentiation between the two species and that there was low intrapopulation differentiation of the species over the 3 years. The results of linkage disequilibrium analyses are consistent with an epidemic genetic structure for both species, with frequent genetic exchange taking place within conspecific populations but not between the R. etli and R. gallicum populations. A subsample of isolates was selected and used for 16S ribosomal DNA PCR-restriction fragment length polymorphism analysis, nifH copy number determination, and host range experiments. Plasmid profiles and nifH hybridization patterns also revealed the occurrence of lateral plasmid transfer among distinct multilocus genotypes within species but not between species. Both species were recovered from nodules of the same plants, indicating that mechanisms other than host, spatial, or temporal isolation may account for the genetic barrier between the species. The biogeographic implications of finding an R. gallicum bv. gallicum population nodulating common bean in America are discussed. PMID:12571008

  20. Rhizobium albus sp. nov., Isolated from Lake Water in Xiamen, Fujian Province of China.

    PubMed

    Li, Yi; Lei, Xueqian; Xu, Yanting; Zhu, Hong; Xu, Meiying; Fu, Lijun; Zheng, Wei; Zhang, Jinli; Zheng, Tianling

    2017-01-01

    A Gram-stain-negative, aerobic bacterial strain, designated Y21(T), was isolated from surface lake water in Xiamen, Fujian Province of China. Growth was observed at temperatures from 4 to 37 °C, at salinities from 0 to 7.0 % and at pH from 6.0 to 10.0. Optimum growth was observed at 28 °C, at pH 7.0 and with 1.5-2.0 % (w/v) NaCl. The highest similarity of 16S rRNA gene sequence between strain Y21(T) and the other strains was 96.9 %. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that the strain was a member of the genus Rhizobium, forming a distinct lineage with R. subbaraonis KCTC 23614(T). The dominant fatty acids were summed feature 8 (comprising C18:1 ω7c and/or C18:1 ω6c), C18:1 ω7c 11-methyl, which accounted for 78.1 %. The G+C content of the chromosomal DNA was 60.9 mol%. The predominant respiratory quinone was ubiquinone-10. The polar lipids of strain Y21(T) were found to consist of five unidentified phospholipids and three unidentified aminolipids. According to its morphology, physiology, fatty acid composition and 16S rRNA sequence data, strain Y21(T) should be regarded as a new species of the genus Rhizobium, for which Rhizobium albus sp. nov. is proposed (type strain Y21(T) = MCCC 1F01210(T) = KCTC 42252(T)).

  1. Phylogenetic diversity of Rhizobium strains nodulating diverse legume species growing in Ethiopia.

    PubMed

    Degefu, Tulu; Wolde-meskel, Endalkachew; Frostegård, Åsa

    2013-06-01

    The taxonomic diversity of thirty-seven Rhizobium strains, isolated from nodules of leguminous trees and herbs growing in Ethiopia, was studied using multilocus sequence analyses (MLSA) of six core and two symbiosis-related genes. Phylogenetic analysis based on the 16S rRNA gene grouped them into five clusters related to nine Rhizobium reference species (99-100% sequence similarity). In addition, two test strains occupied their own independent branches on the phylogenetic tree (AC86a2 along with R. tibeticum; 99.1% similarity and AC100b along with R. multihospitium; 99.5% similarity). One strain from Milletia ferruginea was closely related (>99%) to the genus Shinella, further corroborating earlier findings that nitrogen-fixing bacteria are distributed among phylogenetically unrelated taxa. Sequence analyses of five housekeeping genes also separated the strains into five well-supported clusters, three of which grouped with previously studied Ethiopian common bean rhizobia. Three of the five clusters could potentially be described into new species. Based on the nifH genes, most of the test strains from crop legumes were closely related to several strains of Ethiopian common bean rhizobia and other symbionts of bean plants (R. etli and R. gallicum sv. phaseoli). The grouping of the test strains based on the symbiosis-related genes was not in agreement with the housekeeping genes, signifying differences in their evolutionary history. Our earlier studies revealing a large diversity of Mesorhizobium and Ensifer microsymbionts isolated from Ethiopian legumes, together with the results from the present analysis of Rhizobium strains, suggest that this region might be a potential hotspot for rhizobial biodiversity.

  2. Rhizobium hidalgonense sp. nov., a nodule endophytic bacterium of Phaseolus vulgaris in acid soil.

    PubMed

    Yan, Jun; Yan, Hui; Liu, Li Xue; Chen, Wen Feng; Zhang, Xiao Xia; Verástegui-Valdés, Myrthala M; Wang, En Tao; Han, Xiao Zeng

    2017-01-01

    One Gram-negative, aerobic, motile, rod-shaped bacterium, designated as FH14(T), was isolated from nodules of Phaseolus vulgaris grown in Hidalgo State of Mexico. Results based upon 16S rRNA gene (≥99.8 % similarities to known species), concatenated sequence (recA, atpD and glnII) analysis of three housekeeping genes (≤93.4 % similarities to known species) and average nucleotide identity (ANI) values of genome sequence (ranged from 87.6 to 90.0 % to related species) indicated the distinct position of strain FH14(T) within the genus Rhizobium. In analyses of symbiotic genes, only nitrogen fixation gene nifH was amplified that had nucleotide sequence identical to those of the bean-nodulating strains in R. phaseoli and R. vallis, while nodulation gene nodC gene was not amplified. The failure of nodulation to its original host P. vulgaris and other legumes evidenced the loss of its nodulation capability. Strain FH14(T) contained summed feature 8 (C18:1 ω6c/C18:1 ω7c, 59.96 %), C16:0 (10.6 %) and summed feature 2 (C12:0 aldehyde/unknown 10.928, 10.24 %) as the major components of cellular fatty acids. Failure to utilize alaninamide, and utilizing L-alanine, L-asparagine and γ-amino butyric acid as carbon source, distinguished the strain FH14(T) from the type strains for the related species. The genome size and DNA G+C content of FH14(T) were 6.94 Mbp and 60.8 mol %, respectively. Based on those results, a novel specie in Rhizobium, named Rhizobium hidalgonense sp. nov., was proposed, with FH14(T) (=HAMBI 3636(T) = LMG 29288(T)) as the type strain.

  3. 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

  4. 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

  5. Prediction, identification, and artificial selection of DNA rearrangements in Rhizobium: toward a natural genomic design.

    PubMed

    Flores, M; Mavingui, P; Perret, X; Broughton, W J; Romero, D; Hernández, G; Dávila, G; Palacios, R

    2000-08-01

    Based on the DNA sequence of the symbiotic plasmid of Rhizobium strain NGR234, we predicted potential rearrangements generated by homologous recombination. All predicted rearrangements were identified experimentally by using a PCR-based methodology. Thus, the predicted and the actual dynamic maps of the replicon coincide. By using an approach that does not involve the introduction of exogenous genetic elements, derivative populations that are pure for specific rearrangements were obtained. We propose that knowledge of the DNA sequence of a genome offers the possibility of designing pathways of sequential rearrangements leading to alternative genomic structures. An experimental strategy to isolate bacterial populations containing the desired structures is discussed.

  6. 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.

  7. Improved production of 2'-fucosyllactose in engineered Escherichia coli by expressing putative α-1,2-fucosyltransferase, WcfB from Bacteroides fragilis.

    PubMed

    Chin, Young-Wook; Kim, Ji-Yeong; Kim, Jae-Han; Jung, Sang-Min; Seo, Jin-Ho

    2016-12-02

    2'-Fucosyllactose (2-FL) is one of most abundant oligosaccharides in human milk, which is involved in many biological functions for infant health. Since 2-FL has a great potential in application to functional food materials and pharmaceuticals, several microbial systems for mass production of 2-FL have been developed in recent years. Microbial production of 2-FL was suggested to be influenced by a number of factors including fucosylation activity of α-1,2-fucosyltransferase. In the present study, the wcfB gene coding for α-1,2-fucosyltransferase from Bacteroides fragilis was screened from eleven candidates of putative α-1,2-fucosyltransferase. Introduction of the wcfB gene allows the lacZ-deleted strain of E. coli expressing the genes for guanosine 5'-diphosphate (GDP)-l-fucose biosynthetic enzymes to produce 2-FL. As a result of fed-batch fermentation, 15.4g/L extracellular concentration of 2-FL with 2-FL yield of 0.858g/g lactose and productivity of 0.530g/L/h were obtained. In addition, the feasibility of industrial production of 2-FL using this microbial system was demonstrated by performing fed-batch fermentation in a 75L bioreactor.

  8. Effect of the corn silage to grass silage ratio and feed particle size of diets for ruminants on the ruminal Bacteroides-Prevotella community in vitro.

    PubMed

    Witzig, M; Boguhn, J; Kleinsteuber, S; Fetzer, I; Rodehutscord, M

    2010-08-01

    This study examined whether different corn silage to grass silage ratios in ruminant rations and different grinding levels of the feed affect the composition of the ruminal Bacteroides-Prevotella community in vitro. Three diets, composed of 10% soybean meal as well as of different corn silage and grass silage proportions, were ground through 1mm or 4mm screened sieves and incubated in a semi-continuous rumen simulation system. On day 14 of the incubation microbes were harvested by centrifugation from the liquid effluent of fermenter vessels. Microbial DNA was extracted for single strand conformation polymorphism (SSCP) analysis of 16S rRNA genes followed by sequencing of single SSCP bands. Fluorescence in situ hybridization (FISH) and real-time quantitative (q) PCR were used to quantify differences in the relative abundance of Bacteroides-Prevotella and Prevotella bryantii. SSCP profiles revealed a significant influence of the forage source as well as of the feed particle size on the community structure of the Bacteroides-Prevotella group. Different, phylogenetically distinct, so far uncultured Prevotella species were detected by sequence analysis of several treatment-dependent occurring SSCP bands indicating different nutritional requirements of these organisms for growth. No quantitative differences in the occurrence of Bacteroides-Prevotella-related species were detected between diets by FISH with probe BAC303. However, real-time qPCR data revealed a higher abundance of P. bryantii with increasing grass silage to corn silage ratio, thus again indicating changes within the community composition of the Bacteroides-Prevotella group. As P. bryantii possesses high proteolytic activity its higher abundance may have been caused by the higher contents of crude protein in the grass silage containing diets. To conclude, results of this study show an influence of the forage source on the ruminal community of Bacteroides-Prevotella. Furthermore, they suggest an effect of

  9. Overexpression of BetS, a Sinorhizobium meliloti high-affinity betaine transporter, in bacteroids from Medicago sativa nodules sustains nitrogen fixation during early salt stress adaptation.

    PubMed

    Boscari, Alexandre; Van de Sype, Ghislaine; Le Rudulier, Daniel; Mandon, Karine

    2006-08-01

    Sinorhizobium meliloti possesses several betaine transporters to cope with salt stress, and BetS represents a crucial high-affinity glycine and proline betaine uptake system involved in the rapid acquisition of betaines by cells subjected to osmotic upshock. Using a transcriptional lacZ (beta-galactosidase) fusion, we showed that betS is expressed during the establishment of the symbiosis and in mature nitrogen-fixing nodules. However, neither Nod nor Fix phenotypes were impaired in a betS mutant. BetS is functional in isolated bacteroids, and its activity is strongly activated by high osmolarity. In bacteroids from a betS mutant, glycine betaine and proline betaine uptake was reduced by 85 to 65%, indicating that BetS is a major component of the overall betaine uptake activity in bacteroids in response to osmotic stress. Upon betS overexpression (strain UNA349) in free-living cells, glycine betaine transport was 2.3-fold higher than in the wild-type strain. Interestingly, the accumulation of proline betaine, the endogenous betaine synthesized by alfalfa plants, was 41% higher in UNA349 bacteroids from alfalfa plants subjected to 1 week of salinization (0.3 M NaCl) than in wild-type bacteroids. In parallel, a much better maintenance of nitrogen fixation activity was observed in 7-day-salinized plants nodulated with the overexpressing strain than in wild-type nodulated plants. Taken altogether, these results are consistent with the major role of BetS as an emergency system involved in the rapid uptake of betaines in isolated and in planta osmotically stressed bacteroids of S. meliloti.

  10. A tetracycline efflux gene on Bacteroides transposon Tn4400 does not contribute to tetracycline resistance.

    PubMed Central

    Speer, B S; Salyers, A A

    1990-01-01

    Previously, we demonstrated that the Bacteroides transposon Tn4351, which confers tetracycline resistance only on aerobically grown Escherichia coli, carries a gene that codes for a tetracycline-inactivating enzyme (B. S. Speer and A. A. Salyers, J. Bacteriol. 170:1423-1429, 1988). However, Park et al. (B. H. Park, M. Hendricks, M. H. Malamy, F. P. Tally, and S. B. Levy, Antimicrob. Agents Chemother. 31:1739-1743, 1987) showed that E. coli carrying a closely related transposon, Tn4400, exhibits energy-dependent efflux of tetracycline as well as tetracycline-inactivating activity (B. H. Park and S. B. Levy, Antimicrob. Agents Chemother. 32:1797-1800, 1988). This result raised the question of whether efflux or inactivation or a combination of the two was necessary for resistance conferred by both transposons. We showed that cells carrying Tn4351 did not exhibit the clear-cut efflux activity seen with cells carrying Tn4400 but rather exhibited a tetracycline accumulation profile which could be explained solely on the basis of inactivation of tetracycline in the cytoplasm and rapid diffusion of altered tetracycline out of the cell. Additionally, we were able to clone the efflux and tetracycline-modifying genes of Tn4400 separately. The region carrying the efflux gene spanned one of the two regions in which Tn4400 differs from Tn4351. A clone containing the corresponding region of Tn4351 did not exhibit efflux. Thus, it appears that Tn4351 does not have the efflux gene and that efflux makes no contribution to the resistance conferred by Tn4351. The MIC for cells carrying the subclone from Tn4400 that contained only the gene for tetracycline inactivation was the same that for cells carrying both the inactivation and efflux genes. Cells carrying only the gene for tetracycline efflux were tetracycline sensitive. This was true even when the efflux gene was on a high-copy-number plasmid which increased the level of efflux to that associated with the Tcr gene on pBR328. These

  11. 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.

  12. 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

  13. Galactomannan Catabolism Conferred by a Polysaccharide Utilization Locus of Bacteroides ovatus

    PubMed Central

    Bågenholm, Viktoria; Reddy, Sumitha K.; Bouraoui, Hanene; Morrill, Johan; Kulcinskaja, Evelina; Bahr, Constance M.; Aurelius, Oskar; Rogers, Theresa; Xiao, Yao; Logan, Derek T.; Martens, Eric C.; Koropatkin, Nicole M.; Stålbrand, Henrik

    2017-01-01

    A recently identified polysaccharide utilization locus (PUL) from Bacteroides ovatus ATCC 8483 is transcriptionally up-regulated during growth on galacto- and glucomannans. It encodes two glycoside hydrolase family 26 (GH26) β-mannanases, BoMan26A and BoMan26B, and a GH36 α-galactosidase, BoGal36A. The PUL also includes two glycan-binding proteins, confirmed by β-mannan affinity electrophoresis. When this PUL was deleted, B. ovatus was no longer able to grow on locust bean galactomannan. BoMan26A primarily formed mannobiose from mannan polysaccharides. BoMan26B had higher activity on galactomannan with a high degree of galactosyl substitution and was shown to be endo-acting generating a more diverse mixture of oligosaccharides, including mannobiose. Of the two β-mannanases, only BoMan26B hydrolyzed galactoglucomannan. A crystal structure of BoMan26A revealed a similar structure to the exo-mannobiohydrolase CjMan26C from Cellvibrio japonicus, with a conserved glycone region (−1 and −2 subsites), including a conserved loop closing the active site beyond subsite −2. Analysis of cellular location by immunolabeling and fluorescence microscopy suggests that BoMan26B is surface-exposed and associated with the outer membrane, although BoMan26A and BoGal36A are likely periplasmic. In light of the cellular location and the biochemical properties of the two characterized β-mannanases, we propose a scheme of sequential action by the glycoside hydrolases encoded by the β-mannan PUL and involved in the β-mannan utilization pathway in B. ovatus. The outer membrane-associated BoMan26B initially acts on the polysaccharide galactomannan, producing comparably large oligosaccharide fragments. Galactomanno-oligosaccharides are further processed in the periplasm, degalactosylated by BoGal36A, and subsequently hydrolyzed into mainly mannobiose by the β-mannanase BoMan26A. PMID:27872187

  14. Suppression of colorectal tumorigenesis by recombinant Bacteroides fragilis enterotoxin-2 in vivo

    PubMed Central

    Lv, You; Ye, Tao; Wang, Hui-Peng; Zhao, Jia-Ying; Chen, Wen-Jie; Wang, Xin; Shen, Chen-Xia; Wu, Yi-Bin; Cai, Yuan-Kun

    2017-01-01

    AIM To evaluate the impact of recombinant Bacteroides fragilis enterotoxin-2 (BFT-2, or Fragilysin) on colorectal tumorigenesis in mice induced by azoxymethane/dextran sulfate sodium (AOM/DSS). METHODS Recombinant proBFT-2 was expressed in Escherichia coli strain Rosetta (DE3) and BFT-2 was obtained and tested for its biological activity via colorectal adenocarcinoma cell strains SW-480. Seventy C57BL/6J mice were randomly divided into a blank (BC; n = 10), model (AD; n = 20), model + low-dose toxin (ADLT; n = 20, 10 μg), and a model + high-dose toxin (ADHT; n = 20, 20 μg) group. Mice weight, tumor formation and pathology were analyzed. Immunohistochemistry determined Ki-67 and Caspase-3 expression in normal and tumor tissues of colorectal mucosa. RESULTS Recombinant BFT-2 was successfully obtained, along with its biological activity. The most obvious weight loss occurred in the AD group compared with the ADLT group (21.82 ± 0.68 vs 23.23 ± 0.91, P < 0.05) and the ADHT group (21.82 ± 0.68 vs 23.57 ± 1.06, P < 0.05). More tumors were found in the AD group than in the ADLT and ADHT groups (19.75 ± 3.30 vs 6.50 ± 1.73, P < 0.05; 19.75 ± 3.30 vs 6.00 ± 2.16, P < 0.05). Pathology showed that 12 mice had adenocarcinoma and 6 cases had adenoma in the AD group. Five mice had adenocarcinoma and 15 had adenoma in the ADLT group. Four mice had adenocarcinoma and 16 had adenoma in the ADHT group. The incidence of colorectal adenocarcinoma in both the ADHT group and the ADHT group was reduced compared to that in the AD group (P < 0.05, P < 0.05). The positive rate of Ki-67 in the ADLT group and the ADHT group was 50% and 40%, respectively, both of which were lower than that found in the AD group (94.44%, P < 0.05, P < 0.05). Caspase-3 expression in the ADLT group and the ADHT group was 45% and 55%, both of which were higher than that found in the BC group (16.67%, P < 0.05, P < 0.05). CONCLUSION Oral administration with lower-dose biologically active recombinant BFT-2

  15. 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

  16. Purification and properties of a 75-kilodalton major protein, an immunodominant surface antigen, from the oral anaerobe Bacteroides gingivalis.

    PubMed Central

    Yoshimura, F; Watanabe, K; Takasawa, T; Kawanami, M; Kato, H

    1989-01-01

    A 75-kilodalton major protein (75K protein) was purified to homogeneity from the cell lysate fraction and the envelope of Bacteroides gingivalis 381. The 75K protein was originally present in the outer membrane or the outermost part of this organism as a large, stable complex with an apparent molecular weight of about 2,000,000. Heating at 80 degrees C and at higher temperatures in the presence of sodium dodecyl sulfate was needed to completely dissociate it to monomers. Amino acid analysis revealed that the 75K protein had about 50% nonpolar amino acids. Various strains of B. gingivalis but not other bacteria, including oral Bacteroides species tested, contained serologically related 75K proteins when tested in Western blotting (immunoblotting) analysis. The abundance and localization of the 75K protein in this organism suggest that it has the potential to participate in the host-parasite interaction in infection. The 75K protein was, indeed, strongly recognized in patients with adult periodontal diseases. Immunoblotting with sera from patients and with rabbit antisera generated by intravenous inoculations of whole B. gingivalis cells revealed that the 75K protein was an immunodominant antigen on the surface of B. gingivalis. Images PMID:2553610

  17. Characterization of Glycosaminoglycan (GAG) Sulfatases from the Human Gut Symbiont Bacteroides thetaiotaomicron Reveals the First GAG-specific Bacterial Endosulfatase*

    PubMed Central

    Ulmer, Jonathan E.; Vilén, Eric Morssing; Namburi, Ramesh Babu; Benjdia, Alhosna; Beneteau, Julie; Malleron, Annie; Bonnaffé, David; Driguez, Pierre-Alexandre; Descroix, Karine; Lassalle, Gilbert; Le Narvor, Christine; Sandström, Corine; Spillmann, Dorothe; Berteau, Olivier

    2014-01-01

    Despite the importance of the microbiota in human physiology, the molecular bases that govern the interactions between these commensal bacteria and their host remain poorly understood. We recently reported that sulfatases play a key role in the adaptation of a major human commensal bacterium, Bacteroides thetaiotaomicron, to its host (Benjdia, A., Martens, E. C., Gordon, J. I., and Berteau, O. (2011) J. Biol. Chem. 286, 25973–25982). We hypothesized that sulfatases are instrumental for this bacterium, and related Bacteroides species, to metabolize highly sulfated glycans (i.e. mucins and glycosaminoglycans (GAGs)) and to colonize the intestinal mucosal layer. Based on our previous study, we investigated 10 sulfatase genes induced in the presence of host glycans. Biochemical characterization of these potential sulfatases allowed the identification of GAG-specific sulfatases selective for the type of saccharide residue and the attachment position of the sulfate group. Although some GAG-specific bacterial sulfatase activities have been described in the literature, we report here for the first time the identity and the biochemical characterization of four GAG-specific sulfatases. Furthermore, contrary to the current paradigm, we discovered that B. thetaiotaomicron possesses an authentic GAG endosulfatase that is active at the polymer level. This type of sulfatase is the first one to be identified in a bacterium. Our study thus demonstrates that bacteria have evolved more sophisticated and diverse GAG sulfatases than anticipated and establishes how B. thetaiotaomicron, and other major human commensal bacteria, can metabolize and potentially tailor complex host glycans. PMID:25002587

  18. Bacteroides intestinalis DSM 17393, a member of the human colonic microbiome, upregulates multiple endoxylanases during growth on xylan

    PubMed Central

    Wang, Kui; Pereira, Gabriel V.; Cavalcante, Janaina J. V.; Zhang, Meiling; Mackie, Roderick; Cann, Isaac

    2016-01-01

    Many human diets contain arabinoxylan, and the ease of genome sequencing coupled with reduced cost have led to unraveling the arsenal of genes utilized by the colonic Bacteroidetes to depolymerize this polysaccharide. The colonic Bacteroidetes with potential to ferment arabinoxylans include Bacteroides intestinalis. In this study, we analyzed the hydrolytic activities of members of a xylan degradation cluster encoded on the genome of Bacteroides intestinalis DSM 17393. Here, it is demonstrated that a cocktail of the xylanolytic enzymes completely hydrolyze arabinoxylans found in human diets. We show that this bacterium and relatives have evolved and secrete a unique bifunctional endoxylanase/arabinofuranosidase in the same polypeptide. The bifunctional enzyme and other secreted enzymes attack the polysaccharides extracellularly to remove the side-chains, exposing the xylan backbone for cleavage to xylo-oligosaccharides and xylose. These end products are transported into the cell where a β-xylosidase cleaves the oligosaccharides to fermentable sugars. While our experiments focused on B. intestinalis, it is likely that the extracellular enzymes also release nutrients to members of the colonic microbial community that practice cross-feeding. The presence of the genes characterized in this study in other colonic Bacteroidetes suggests a conserved strategy for energy acquisition from arabinoxylan, a component of human diets. PMID:27681607

  19. Rhizobium hedysari sp. nov., a novel species isolated from a root nodule of Hedysarum multijugum in China.

    PubMed

    Xu, Lin; Shi, Jianfeng; Li, Caixia; Zhu, Shengan; Li, Bo

    2017-04-01

    A strain 5-1-2(T) was isolated from a root nodule of Hedysarum multijugum collected from Zhangye city, Gansu province, north-west China. Phylogenetic analysis based on the 16S rRNA gene sequence and other housekeeping genes (recA and atpD) indicated that the strain represents a novel species in the genus Rhizobium close to the strain Rhizobium subbaraonis JC85(T) with similarities of 98.27, 88.92 and 89.62%, respectively. Strain 5-1-2(T) contained Q-10 as the predominant ubiquinone. Our results showed that the major fatty acids were feature 8 (C18:1 ω7c and/or C18:1 ω6c; 38.90%). In addition, the DNA-DNA hybridizations with the type strains R. subbaraonis JC85(T) and Rhizobium halophytocola YC6881(T) were 39.2 ± 2.1 and 44.3 ± 1.9, respectively. Therefore, a novel species Rhizobium hedysari sp. nov. is proposed, and 5-1-2(T) (=CGMCC1.15677(T) = NBRC112532(T)) is designated as the type strain.

  20. 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.

  1. Population Densities of Rhizobium japonicum Strain 123 Estimated Directly in Soil and Rhizospheres †

    PubMed Central

    Reyes, V. G.; Schmidt, E. L.

    1979-01-01

    Rhizobium japonicum serotype 123 was enumerated in soil and rhizospheres by fluorescent antibody techniques. Counting efficiency was estimated to be about 30%. Indigenous populations of strain 123 ranged from a few hundred to a few thousand per gram of field soil before planting. Rhizosphere effects from field-grown soybean plants were modest, reaching a maximum of about 2 × 104 cells of strain 123 per g of inner rhizosphere soil in young (16-day-old) plants. Comparably slight rhizosphere stimulation was observed with field corn. High populations of strain 123 (2 × 106 to 3 × 106 cells per g) were found only in the disintegrating taproot rhizospheres of mature soybeans at harvest, and these populations declined rapidly after harvest. Pot experiments with the same soil provided data similar to those derived from the field experiments. Populations of strain 123 reached a maximum of about 105 cells per g of soybean rhizosphere soil, but most values were lower and were only slightly higher than values in wheat rhizosphere soil. Nitrogen treatments had little effect on strain 123 densities in legume and nonlegume rhizospheres or on the nodulation success of strain 123. No evidence was obtained for the widely accepted theory of specific stimulation, which has been proposed to account for the initiation of the Rhizobium-legume symbiosis. PMID:16345383

  2. 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.

  3. Production of proteasome inhibitor syringolin A by the endophyte Rhizobium sp. strain AP16.

    PubMed

    Dudnik, Alexey; Bigler, Laurent; Dudler, Robert

    2014-06-01

    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.

  4. Symbiont shift towards Rhizobium nodulation in a group of phylogenetically related Phaseolus species.

    PubMed

    Servín-Garcidueñas, Luis E; Zayas-Del Moral, Alejandra; Ormeño-Orrillo, Ernesto; Rogel, Marco A; Delgado-Salinas, Alfonso; Sánchez, Federico; Martínez-Romero, Esperanza

    2014-10-01

    Bean plants from the Phaseolus genus are widely consumed and represent a nitrogen source for human nutrition. They provide biological fertilization by establishing root nodule symbiosis with nitrogen-fixing bacteria. To establish a successful interaction, bean plants and their symbiotic bacteria need to synchronize a proper molecular crosstalk. Within the Phaseolus genus, P. vulgaris has been the prominent species to study nodulation with Rhizobium symbionts. However the Phaseolus genus comprises diverse species whose symbionts have not been analyzed. Here we identified and studied nodule bacteria from representative Phaseolus species not previously analyzed and from all the described wild species related to P. vulgaris. We found Bradyrhizobium in nodules from most species representing all Phaseolus clades except in five phylogenetically related species from the P. vulgaris clade. Therefore we propose that Bradyrhizobium nodulation is common in Phaseolus and that there was a symbiont preference shift to Rhizobium nodulation in few related species. This work sets the basis to further study the genetic basis of this symbiont substitution.

  5. Joint evolution of kin recognition and cooperation in spatially structured rhizobium populations.

    PubMed

    Zee, Peter C; Bever, James D

    2014-01-01

    In the face of costs, cooperative interactions maintained over evolutionary time present a central question in biology. What forces maintain this cooperation? Two potential ways to explain this problem are spatially structured environments (kin selection) and kin-recognition (directed benefits). In a two-locus population genetic model, we investigated the relative roles of spatial structure and kin recognition in the maintenance of cooperation among rhizobia within the rhizobia-legume mutualism. In the case where the cooperative and kin recognition loci are independently inherited, spatial structure alone maintains cooperation, while kin recognition decreases the equilibrium frequency of cooperators. In the case of co-inheritance, spatial structure remains a stronger force, but kin recognition can transiently increase the frequency of cooperators. Our results suggest that spatial structure can be a dominant force in maintaining cooperation in rhizobium populations, providing a mechanism for maintaining the mutualistic nodulation trait. Further, our model generates unique and testable predictions that could be evaluated empirically within the legume-rhizobium mutualism.

  6. 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

  7. Revegetating fly ash landfills with Prosopis juliflora L.: impact of different amendments and Rhizobium inoculation.

    PubMed

    Rai, U N; Pandey, K; Sinha, S; Singh, A; Saxena, R; Gupta, D K

    2004-05-01

    A revegetation trial was conducted to evaluate the feasibility of growing a legume species, Prosopis juliflora L., on fly ash ameliorated with combination of various organic amendments, blue-green algal biofertilizer and Rhizobium inoculation. Significant enhancements in plant biomass, photosynthetic pigments, protein content and in vivo nitrate reductase activity were found in the plants grown on ameliorated fly ash in comparison to the plants growing in unamended fly ash or garden soil. Higher growth was obtained in fly ash amended with blue-green algae (BGA) than farmyard manure or press mud (PM), a waste from sugar-processing industry, due to the greater contribution of plant nutrients, supply of fixed nitrogen and increased availability of phosphorus. Nodulation was suppressed in different amendments of fly ash with soil in a concentration-duration-dependent manner, but not with other amendments. Plants accumulated higher amounts of Fe, Mn, Cu, Zn and Cr in various fly ash amendments than in garden soil. Further, inoculation of the plant with a fly ash tolerant Rhizobium strain conferred tolerance for the plant to grow under fly ash stress conditions with more translocation of metals to the above ground parts. The results showed the potential of P. juliflora to grow in plantations on fly ash landfills and to reduce the metal contents of fly ash by bioaccumulation in its tissues.

  8. Structural complexity of the symbiotic plasmid of Rhizobium leguminosarum bv. phaseoli.

    PubMed Central

    Girard, M L; Flores, M; Brom, S; Romero, D; Palacios, R; Dávila, G

    1991-01-01

    The complete physical map of the symbiotic plasmid of Rhizobium leguminosarum bv. phaseoli strain CFN42 was established. The data support the concept that Rhizobium symbiotic genes are part of a complex genomic structure which contains a large amount of reiterated DNA sequences. This plasmid is a circular structure of 390 kb with approximately 10 families of internally reiterated DNA sequences of two to three elements each. One family includes two directly oriented nitrogenase operons situated 120 kb apart. We also found several stretches of pSym that are reiterated in other replicons of the cell. Localization of symbiotic gene sequences by heterologous hybridization revealed that nodABC sequences are separated in two regions, each of which contains a nod boxlike element, and it also suggested the presence of two copies of the nifA and nodD gene sequences. We propose that the complex structure of the symbiotic plasmid allows interactions between repeated DNA sequences which, in turn, might result in frequent rearrangements. Images PMID:2013564

  9. Canonical ordered cosmid library of the symbiotic plasmid of Rhizobium species NGR234.

    PubMed Central

    Perret, X; Broughton, W J; Brenner, S

    1991-01-01

    Many of the bacterial genes involved in nodulation (nod) and nitrogen fixation (nif) are dispersed over the 500-kilobase plasmid pNGR234a of the broad host-range Rhizobium species NGR234. As a first step toward generating a complete physical and genetic map of the plasmid, a full overlapping collection of cosmids was derived from a total genomic library. Clones were aligned by combining fingerprinting, hybridization, and pulsed-field gel electrophoresis data. Symbiotic loci were localized by probing a representative set of cosmids with both homologous and heterologous genes. nodABC, nodD1, nodD2, nodSU, nolB, and region II are widely dispersed over pNGR234a, while the two functional copies of nifKDH are separated by only 28 kilobases. Interestingly, sequences homologous to nodE, nodG, nodP, and nodQ have been assigned to another autonomously replicating element in Rhizobium species NGR234. Similarly one copy of the structural dctA gene is located on the symbiotic plasmid (dctA1) while the other is on what we assume to be the chromosome. Images PMID:2000397

  10. 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.

  11. 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

  12. Rhizobium ecuadorense sp. nov., an indigenous N2-fixing symbiont of the Ecuadorian common bean (Phaseolus vulgaris L.) genetic pool.

    PubMed

    Ribeiro, Renan Augusto; Martins, Talita Busulini; Ormeño-Orrillo, Ernesto; Marçon Delamuta, Jakeline Renata; Rogel, Marco Antonio; Martínez-Romero, Esperanza; Hungria, Mariangela

    2015-09-01

    There are two major centres of genetic diversification of common bean (Phaseolus vilgaris L.), the Mesoamerican and the Andean, and the legume is capable of establishing nitrogen-fixing symbioses with several rhizobia; Rhizobium etli seems to be the dominant species in both centres. Another genetic pool of common bean, in Peru and Ecuador, is receiving increasing attention, and studies of microsymbionts from the region can help to increase our knowledge about coevolution of this symbiosis. We have previously reported several putative new lineages from this region and here present data indicating that strains belonging to one of them, PEL4, represent a novel species. Based on 16S rRNA gene sequence phylogeny, PEL4 strains are positioned in the Rhizobium phaseoli/R. etli/Rhizobium leguminosarum clade, but show unique properties in several morphological, physiological and biochemical analyses, as well as in BOX-PCR profiles ( < 75% similarity with related species). PEL4 strains also differed from related species based on multilocus sequence analysis of three housekeeping genes (glnII, gyrB and recA). Nucleotide identities of the three concatenated genes between PEL4 strains and related species ranged from 91.8 to 94.2%, being highest with Rhizobium fabae. DNA-DNA hybridization ( < 47% DNA relatedness) and average nucleotide identity values of the whole genomes ( < 90.2%) also supported the novel species status. The PEL4 strains were effective in nodulating and fixing N2 with common beans. The data supported the view that PEL4 strains represent a novel species, Rhizobium ecuadorense sp. nov. The type strain is CNPSo 671(T) ( = UMR 1450(T) = PIMAMPIRS I 5(T) = LMG 27578(T)).

  13. A Rhizobium leguminosarum CHDL- (Cadherin-Like-) Lectin Participates in Assembly and Remodeling of the Biofilm Matrix

    PubMed Central

    Vozza, Nicolás F.; Abdian, Patricia L.; Russo, Daniela M.; Mongiardini, Elías J.; Lodeiro, Aníbal R.; Molin, Søren; Zorreguieta, Angeles

    2016-01-01

    In natural environments most bacteria live in multicellular structures called biofilms. These cell aggregates are enclosed in a self-produced polymeric extracellular matrix, which protects the cells, provides mechanical stability and mediates cellular cohesion and adhesion to surfaces. Although important advances were made in the identification of the genetic and extracellular factors required for biofilm formation, the mechanisms leading to biofilm matrix assembly, and the roles of extracellular proteins in these processes are still poorly understood. The symbiont Rhizobium leguminosarum requires the synthesis of the acidic exopolysaccharide and the PrsDE secretion system to develop a mature biofilm. PrsDE is responsible for the secretion of the Rap family of proteins that share one or two Ra/CHDL (cadherin-like-) domains. RapA2 is a calcium-dependent lectin with a cadherin-like β sheet structure that specifically recognizes the exopolysaccharide, either as a capsular polysaccharide (CPS) or in its released form [extracellular polysaccharide (EPS)]. In this study, using gain and loss of function approaches combined with phenotypic and microscopic studies we demonstrated that RapA lectins are involved in biofilm matrix development and cellular cohesion. While the absence of any RapA protein increased the compactness of bacterial aggregates, high levels of RapA1 expanded distances between cells and favored the production of a dense matrix network. Whereas endogenous RapA(s) are predominantly located at one bacterial pole, we found that under overproduction conditions, RapA1 surrounded the cell in a way that was reminiscent of the capsule. Accordingly, polysaccharide analyses showed that the RapA lectins promote CPS formation at the expense of lower EPS production. Besides, polysaccharide analysis suggests that RapA modulates the EPS size profile. Collectively, these results show that the interaction of RapA lectins with the polysaccharide is involved in rhizobial

  14. Inoculant Production with Diluted Liquid Cultures of Rhizobium spp. and Autoclaved Peat: Evaluation of Diluents, Rhizobium spp., Peats, Sterility Requirements, Storage, and Plant Effectiveness

    PubMed Central

    Somasegaran, P.

    1985-01-01

    Fully grown broth cultures of various fast- and slow-growing rhizobia were deliberately diluted with various diluents before their aseptic incorporation into autoclaved peat in polypropylene bags (aseptic method) or mixed with the peat autoclaved in trays (tray method). In a factorial experiment with the aseptic method, autoclaved and irradiated peat samples from five countries were used to prepare inoculants with water-diluted cultures of three Rhizobium spp. When distilled water was used as the diluent, the multiplication and survival of rhizobia in the peat was similar to that with diluents having a high nutrient status when the aseptic method was used. In the factorial experiment, the mean viable counts per gram of inoculant were log 9.23 (strain TAL 102) > log 8.92 (strain TAL 82) > log 7.89 (strain TAL 182) after 24 weeks of storage at 28°C. The peat from Argentina was the most superior for the three Rhizobium spp., with a mean viable count of log 9.0 per g at the end of the storage period. The quality of inoculants produced with diluted cultures was significantly (P = 0.05) better with irradiated than with autoclaved peat, as shown from the factorial experiment. With the tray method, rhizobia in cultures diluted 1,000-fold or less multiplied and stored satisfactorily in the presence of postinoculation contaminants, as determined by plate counts, membrane filter immunofluorescence, and plant infection procedures. All strains of rhizobia used in both the methods showed various degrees of population decline in the inoculants when stored at 28°C. Fast- and slow-growing rhizobia in matured inoculants produced by the two methods showed significant (P < 0.01) decline in viability when stored at 4°C, whereas the viability of some strains increased significantly (P < 0.01) at the same temperature. The plant effectiveness of inoculants produced with diluted cultures and autoclaved peat did not differ significantly from that of inoculants produced with undiluted

  15. Effect of Rhizobium sp. BARIRGm901 inoculation on nodulation, nitrogen fixation and yield of soybean (Glycine max) genotypes in gray terrace soil.

    PubMed

    Alam, Faridul; Bhuiyan, M A H; Alam, Sadia Sabrina; Waghmode, Tatoba R; Kim, Pil Joo; Lee, Yong Bok

    2015-01-01

    Soybean plants require high amounts of nitrogen, which are mainly obtained from biological nitrogen fixation. A field experiment was conducted by soybean (Glycine max) genotypes, growing two varieties (Shohag and BARI Soybean6) and two advanced lines (MTD10 and BGM02026) of soybean with or without Rhizobium sp. BARIRGm901 inoculation. Soybean plants of all genotypes inoculated with Rhizobium sp. BARIRGm901 produced greater nodule numbers, nodule weight, shoot and root biomass, and plant height than non-inoculated plants. Similarly, inoculated plants showed enhanced activity of nitrogenase (NA) enzyme, contributing to higher nitrogen fixation and assimilation, compared to non-inoculated soybean plants in both years. Plants inoculated with Rhizobium sp. BARIRGm901 also showed higher pod, stover, and seed yield than non-inoculated plants. Therefore, Rhizobium sp. BARIRGm901 established an effective symbiotic relationship with a range of soybean genotypes and thus increased the nodulation, growth, and yield of soybean grown in gray terrace soils in Bangladesh.

  16. Stat3 Activation in Murine Colitis Induced by Enterotoxigenic Bacteroides fragilis

    PubMed Central

    Wick, Elizabeth C.; Rabizadeh, Shervin; Albesiano, Emilia; Wu, XinQun; Wu, Shaoguang; Chan, June; Rhee, Ki-Jong; Ortega, Guillermo; Huso, David L.; Pardoll, Drew; Housseau, Franck; Sears, Cynthia L.

    2014-01-01

    Background Enterotoxigenic Bacteroides fragilis (ETBF), a molecular subclass of the common human commensal, B. fragilis, has been associated with inflammatory bowel disease. ETBF colitis is characterized by the activation of Stat3 and a Th17 immune response in the colonic mucosa. This study was designed to investigate the time course and cellular distribution of Stat3 activation in ETBF-colonized mice. Methods C57BL/6 wild-type, C57BL/6Stat3ΔIEC, or Rag-1 mice were inoculated with saline, nontoxigenic B. fragilis or ETBF. Histologic diagnosis and mucosal Stat activation (immunohistochemistry, Western blot, and/or electrophorectic mobility shift assay) were evaluated over time (6–24 h, 1–7 d, and 1–18 mo after inoculation). Mucosal permeability was evaluated at 16 hours, 1 day, and 3 days. Mucosal immune responses were evaluated at 1 week, and 12 and 18 months. Results ETBF induced rapid-onset colitis that persisted for up to 1 year. Stat3 activation (pStat3) was noted in the mucosal immune cells within 16 hours, with colonic epithelial cell activation evident at 24 hours after inoculation. ETBF-induced increased mucosal permeability was first observed at 24 hours after inoculation, after which the initial immune cell pStat3 activation was noted. Immune cell pStat3 was present in the absence of epithelial pStat3 (C57BL/ 6Stat3ΔIEC). Epithelial pStat3 was present in the absence of T and B cells (Rag-1 mice). pStat3 persisted in the epithelial and immune cells for 1 year, characterized by isolated pStat3-positive cell clusters, with varying intensity distributed through the proximal and distal colon. Similarly, mucosal Th17 immune responses persisted for up to 1 year. Loss of fecal ETBF colonization was associated with the loss of mucosal pStat3 and Th17 immune responses. Conclusions ETBF rapidly induces immune cell pStat3, which is independent of epithelial pStat3. This occurs before ETBF-induced mucosal permeability, suggesting that ETBF, likely through B

  17. 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.

  18. 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

  19. 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.

  20. De novo alanine synthesis by bacteroids of Mesorhizobium loti is not required for nitrogen transfer in the determinate nodules of Lotus corniculatus.

    PubMed

    Kumar, Shalini; Bourdès, Alexandre; Poole, Philip

    2005-08-01

    Deletion of both alanine dehydrogenase genes (aldA) in Mesorhizobium loti resulted in the loss of AldA enzyme activity from cultured bacteria and bacteroids but had no effect on the symbiotic performance of Lotus corniculatus plants. Thus, neither indeterminate pea nodules nor determinate L. corniculatus nodules export alanine as the sole nitrogen secretion product.

  1. 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...

  2. Agonistic and antagonistic properties of a Rhizobium sin-1 lipid A modified by an ether-linked lipid

    PubMed Central

    Vasan, Mahalakshmi; Wolfert, Margreet A.; Boons, Geert-Jan

    2010-01-01

    LPS from Rhizobium sin-1 (R. sin-1) can antagonize the production of tumor necrosis factor alpha (TNF-α) by E. coli LPS in human monocytic cells. Therefore these compounds provide interesting leads for the development of therapeutics for the prevention or treatment of septic shock. Detailed structure activity relationship studies have, however, been hampered by the propensity of these compounds to undergo β-elimination to give biological inactive enone derivatives. To address this problem, we have chemically synthesized in a convergent manner a R. sin-1 lipid A derivative in which the β-hydroxy ester at C-3 of the proximal sugar unit has been replaced by an ether linked moiety. As expected, this derivative exhibited a much-improved chemical stability. Furthermore, its ability to antagonize TNF-α production induced by enteric LPS was only slightly smaller than that of the parent ester modified derivative demonstrating that the ether-linked lipids affect biological activities only marginally. Furthermore, it has been shown for the first time that R. sin-1 LPS and the ether modified lipid A are also able to antagonize the production of the cytokine interferon-inducible protein 10, which arises from the TRIF-dependent pathway. The latter pathway was somewhat more potently inhibited than the MyD88-dependent pathway. Furthermore, it was observed that the natural LPS possesses much greater activity than the synthetic and isolated lipid As, which indicates that di-KDO moiety is important for optimal biological activity. It has also been found that isolated R. sin-1 LPS and lipid A agonize a mouse macrophage cell line to induce the production of TNF-α and interferon beta in a Toll-like receptor 4-dependent manner demonstrating species specific properties. PMID:17581652

  3. The symbiotic bacterial surface factor polysaccharide A on Bacteroides fragilis inhibits IL-1β-induced inflammation in human fetal enterocytes via toll receptors 2 and 4

    PubMed Central

    Jiang, Fei; Meng, Di; Weng, Meiqian; Zhu, Weishu; Wu, Wenxue; Kasper, Dennis; Walker, W. Allan

    2017-01-01

    Colonizing bacteria interacting with the immature, unlike the mature, human intestine favors inflammation over immune homeostasis. As a result, ten percent of premature infants under 1500 grams weight develop an inflammatory necrosis of the intestine after birth, e.g., necrotizing enterocolitis (NEC). NEC is a major health problem in this population causing extensive morbidity and mortality and an enormous expenditure of health care dollars. NEC can be prevented by giving preterm infants their mother’s expressed breast milk or ingesting selective probiotic organisms. Vaginally delivered, breast fed newborns develop health promoting bacteria (“pioneer” bacteria) which preferentially stimulate intestinal host defense and anti-inflammation. One such “pioneer” organism is Bacteroides fragilis with a polysaccharide (PSA) on its capsule. B. fragilis has been shown developmentally in intestinal lymphocytes and dendritic cells to produce a balanced T-helper cell (TH1/TH2) response and to reduce intestinal inflammation by activity through the TLR2 receptor stimulating IL-10 which inhibits IL-17 causing inflammation. No studies have been done on the role of B. fragilis PSA on fetal enterocytes and its increased inflammation. Accordingly, using human and mouse fetal intestinal models, we have shown that B. fragilis with PSA and PSA alone inhibits IL-1β-induced IL-8 inflammation in fetal and NEC intestine. We have also begun to define the mechanism for this unique inflammation noted in fetal intestine. We have shown that B. fragilis PSA anti-inflammation requires both the TLR2 and TLR4 receptor and is in part mediated by the AP1 transcription factor (TLR2) which is developmentally regulated. These observations may help to devise future preventative treatments of premature infants against NEC. PMID:28278201

  4. Effectiveness of halo-tolerant, auxin producing Pseudomonas and Rhizobium strains to improve osmotic stress tolerance in mung bean (Vigna radiata L.).

    PubMed

    Ahmad, Maqshoof; Zahir, Zahir A; Nazli, Farheen; Akram, Fareeha; Arshad, Muhammad; Khalid, Muhammad

    2013-12-01

    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.

  5. Structure of dihydrodipicolinate synthase from the commensal bacterium Bacteroides thetaiotaomicron at 2.1 Å resolution

    PubMed Central

    Mank, Nicholas; Arnette, Amy; Klapper, Vince; Offermann, Lesa; Chruszcz, Maksymilian

    2015-01-01

    Dihydrodipicolinate synthase (DapA) catalyzes the first committed step of the diaminopimelate biosynthetic pathway of lysine. It has been shown to be an essential enzyme in many bacteria and has been the subject of research to generate novel antibiotics. However, this pathway is present in both pathogenic and commensal bacteria, and antibiotics targeting DapA may interfere with normal gut colonization. Bacteroides thetaiotaomicron is a Gram-negative commensal bacterium that makes up a large proportion of the normal microbiota of the human gut. The structure of DapA from B. thetaiotaomicron (BtDapA) has been determined. This structure will help to guide the generation of selectively active antibiotic compounds targeting DapA. PMID:25849508

  6. New cfiA variant and novel insertion sequence elements in carbapenem-resistant Bacteroides fragilis isolates from Korea.

    PubMed

    Roh, Kyoung Ho; Kim, Sinyoung; Kim, Chang-Ki; Yum, Jong Hwa; Kim, Myung Sook; Yong, Dongeun; Jeong, Seok Hoon; Lee, Kyungwon; Kim, June Myung; Chong, Yunsop

    2010-04-01

    Of 276 nonduplicate Bacteroides fragilis clinical isolates recovered from 1997 to 2004, 3 were resistant to carbapenem. cepA and cfiA alleles were detected by polymerase chain reaction in 240 (87.0%) and 11 (4.0%) of the isolates, respectively. Insertion sequence (IS) elements were found only in the 3 carbapenem-resistant B. fragilis isolates, which produced metallo-beta-lactamase at a level detectable by UV spectrophotometry. Sequence analysis showed 1 new cfiA variant, cfiA(11), and 2 novel IS elements. The cfiA(11) gene revealed 5 amino acid substitutions compared to cfiA, with 97.6% amino acid identity. The transposase, terminal inverted repeat sequence, and target site duplication sequence of the 2 novel IS elements were unique. This study reconfirmed the correlation between ISs and carbapenem resistance in B. fragilis.

  7. Scarce detection of mobile erm genes associated with tetQ in Bacteroides and Parabacteroides from Costa Rica.

    PubMed

    Quesada-Gómez, Carlos; Rodríguez-Cavallini, Evelyn; Rodríguez, César

    2013-06-01

    The frequency of finding of clindamycin-resistant anaerobic bacteria in clinical samples has doubled from 2008 to 2010 in Costa Rica. To determine whether this increase is due to dissemination of erm genes aided by tetQ elements, we analyzed 100 isolates of Bacteroides or Parabacteroides from a regional hospital, a national hospital, and the community. Antimicrobial susceptibilities were recorded with a broth micro-dilution method and erm genes were detected by PCR and Southern blotting. In addition, plasmid isolation and mating experiments were performed to clarify the location and mobility of the detected erm genes. Resistance to clindamycin was by far more frequent in the regional hospital (72%) than in the national hospital (29%) and the community (26%). Resistance to tetracycline was even more common, with the community (85%) outweighing the hospitals (71-72%). While MIC of clindamycin were higher in the hospitals than in the community (P < 0.05), the opposite was seen for tetracycline (P < 0.0001). Of the sought-after genes, only ermG (n = 2), ermA (n = 1), and ermF (n = 1) were detected in the hospitals and ermF in the community (n = 2). In opposition to the low frequency of finding of erm genes, 71% of the isolates were positive for tetQ. None of the detected genes were encoded on plasmids. Only three isolates from the hospitals transferred their erm genes laterally. By contrast, 13 hospital isolates and two community isolates transferred tetQ. Despite the widespread finding of tetracycline-resistant tetQ-positive bacteria, mobile erm genes were rare in our bacterial collection. We conclude that the detected erm genes are likely not included in typical conjugative transposons of Bacteroides and Parabacteroides.

  8. Bacteroides uniformis is a putative bacterial species associated with the degradation of the isoflavone genistein in human feces.

    PubMed

    Renouf, Mathieu; Hendrich, Suzanne

    2011-06-01

    Inter-individual variation in isoflavone absorption depends on gut microbial degradation and affects the efficacy of these compounds. We hypothesized that inter-individual variation in fecal isoflavone disappearance coincided with variation in bacterial species. In vitro anaerobic fecal disappearance of isoflavones was measured from 33 participants by HPLC. Fecal microbial 16S rRNA variable region PCR products were obtained from 4 participants with the greatest and least genistein or glycitein degradation and were subjected to denaturing gradient gel electrophoresis. DNA bands with a homology of 90-95% to Bacteroides uniformis and Faecalibacterium prausnitzii were present in greater intensities in fecal samples showing a genistein disappearance rate constant of 1.47 ± 0.14 h(-1) compared with those with a genistein disappearance rate constant of 0.15 ± 0.03 h(-1) (P < 0.05). Human fecal bacterial species with DNA sequences 90-100% homologous to Tannerella forsythensis and 4 other species were present in greater intensities in fecal samples showing a glycitein disappearance rate constant of 0.57 ± 0.30 h(-1) compared with fecal samples with a glycitein disappearance rate constant of 0.08 ± 0.03 h(-1) (P < 0.05). In high degraders, B. uniformis may be a candidate for genistein degradation and T. forsythensis for glycitein degradation, based on fecal isoflavone degradation in the presence of these species. Bacteroides acidifaciens increased isoflavone disappearance in anaerobic human fecal incubations under nutrient-rich and -depleted conditions, suggesting this species as one responsible for the generally high degradation of isoflavones by humans. These fecal microbes are candidate biomarkers for interindividual variation in isoflavone uptake and efficacy.

  9. Function of the Rhizobium etli CFN42 nirK gene in nitrite metabolism.

    PubMed

    Bueno, E; Gómez-Hernández, N; Girard, L; Bedmar, E J; Delgado, M J

    2005-02-01

    Rhizobium etli CFN42 is not capable of growing anaerobically with nitrate but it grows with nitrite as a terminal electron acceptor. This bacterium contains the nirK gene encoding the copper-containing Nir (nitrite reductase), which is located on the cryptic plasmid pCFN42f. Mutational analysis has demonstrated that a nirK deficient mutant was not capable of growing under nitrite-respiring conditions. Moreover, microaerobic growth of this mutant was inhibited by the presence of nitrite. Nir activity and nitrite uptake were highly diminished in a nirK mutant, compared with the wild-type levels after incubation under anaerobic conditions. Our results suggest that the copper-containing Nir may have both a respiratory and a nitrite-detoxifying role in R. etli.

  10. Agrobacterium strains isolated from root nodules of common bean specifically reduce nodulation by Rhizobium gallicum.

    PubMed

    Mrabet, Moncef; Mnasri, Bacem; Romdhane, Samir Ben; Laguerre, Gisèle; Aouani, Mohamed Elarbi; Mhamdi, Ridha

    2006-05-01

    In a previous work, we showed that non-nodulating agrobacteria strains were able to colonize root nodules of common bean. Both rhizobia and agrobacteria co-existed in the infected nodules. No impact on symbiosis was found in laboratory conditions when using sterile gravel as a support for growth. In this study, soil samples originating from different geographic and agronomic regions in Tunisia were inoculated with a mixture of agrobacteria strains isolated previously from root nodules of common bean. A significant effect on nodulation and vegetal growth of common bean was observed. Characterization of nodulating rhizobia and comparison with non-inoculated controls showed a biased genetic structure. It seemed that Rhizobium gallicum was highly inhibited, whereas nodulation by Sinorhizobium medicae was favored. Co-inoculation of non-sterile soils with R. gallicum and agrobacteria confirmed these findings. In vitro antibiosis assays indicated that agrobacteria exercised a significant antagonism against R. gallicum.

  11. 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

  12. Genome sequence of the Trifolium rueppellianum -nodulating Rhizobium leguminosarum bv. trifolii strain WSM2012.

    PubMed Central

    Reeve, Wayne; Melino, Vanessa; Ardley, Julie; Tian, Rui; De Meyer, Sofie; Terpolilli, Jason; Tiwari, Ravi; Yates, Ronald; O’Hara, Graham; Howieson, John; Ninawi, Mohamed; Held, Brittany; Bruce, David; Detter, Chris; Tapia, Roxanne; Han, Cliff; Wei, Chia-Lin; Huntemann, Marcel; Han, James; Chen, I-Min; Mavromatis, Konstantinos; Markowitz, Victor; Szeto, Ernest; Ivanova, Natalia; Mikhailova, Natalia; Pagani, Ioanna; Pati, Amrita; Goodwin, Lynne; Woyke, Tanja; Kyrpides, Nikos

    2013-01-01

    Rhizobium leguminosarum bv. trifolii WSM2012 (syn. MAR1468) is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an ineffective root nodule recovered from the roots of the annual clover Trifolium rueppellianum Fresen growing in Ethiopia. WSM2012 has a narrow, specialized host range for N2-fixation. Here we describe the features of R. leguminosarum bv. trifolii strain WSM2012, together with genome sequence information and annotation. The 7,180,565 bp high-quality-draft genome is arranged into 6 scaffolds of 68 contigs, contains 7,080 protein-coding genes and 86 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:24976885

  13. Genome sequence of the South American clover-nodulating Rhizobium leguminosarum bv. trifolii strain WSM597

    PubMed Central

    Reeve, Wayne; Terpolilli, Jason; Melino, Vanessa; Ardley, Julie; Tian, Rui; De Meyer, Sofie; Tiwari, Ravi; Yates, Ronald; O’Hara, Graham; Howieson, John; Ninawi, Mohamed; Held, Brittany; 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; Woyke, Tanja; Kyrpides, Nikos

    2013-01-01

    Rhizobium leguminosarum bv. trifolii strain WSM597 is an aerobic, motile, Gram-negative, non-spore-forming rod isolated from a root nodule of the annual clover Trifolium pallidum L. growing at Glencoe Research Station near Tacuarembó, Uruguay. This strain is generally ineffective for nitrogen (N2) fixation with clovers of Mediterranean, North American and African origin, but is effective on the South American perennial clover T. polymorphum Poir. Here we describe the features of R. leguminosarum bv. trifolii strain WSM597, together with genome sequence information and annotation. The 7,634,384 bp high-quality-draft genome is arranged in 2 scaffolds of 53 contigs, contains 7,394 protein-coding genes and 87 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:24976883

  14. Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain TA1.

    PubMed

    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

    2013-12-20

    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.

  15. Genome sequence of the South American clover-nodulating Rhizobium leguminosarum bv. trifolii strain WSM597.

    PubMed

    Reeve, Wayne; Terpolilli, Jason; Melino, Vanessa; Ardley, Julie; Tian, Rui; De Meyer, Sofie; Tiwari, Ravi; Yates, Ronald; O'Hara, Graham; Howieson, John; Ninawi, Mohamed; Held, Brittany; 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; Woyke, Tanja; Kyrpides, Nikos

    2013-12-20

    Rhizobium leguminosarum bv. trifolii strain WSM597 is an aerobic, motile, Gram-negative, non-spore-forming rod isolated from a root nodule of the annual clover Trifolium pallidum L. growing at Glencoe Research Station near Tacuarembó, Uruguay. This strain is generally ineffective for nitrogen (N2) fixation with clovers of Mediterranean, North American and African origin, but is effective on the South American perennial clover T. polymorphum Poir. Here we describe the features of R. leguminosarum bv. trifolii strain WSM597, together with genome sequence information and annotation. The 7,634,384 bp high-quality-draft genome is arranged in 2 scaffolds of 53 contigs, contains 7,394 protein-coding genes and 87 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program.

  16. Genome sequence of the Trifolium rueppellianum -nodulating Rhizobium leguminosarum bv. trifolii strain WSM2012.

    PubMed

    Reeve, Wayne; Melino, Vanessa; Ardley, Julie; Tian, Rui; De Meyer, Sofie; Terpolilli, Jason; Tiwari, Ravi; Yates, Ronald; O'Hara, Graham; Howieson, John; Ninawi, Mohamed; Held, Brittany; Bruce, David; Detter, Chris; Tapia, Roxanne; Han, Cliff; Wei, Chia-Lin; Huntemann, Marcel; Han, James; Chen, I-Min; Mavromatis, Konstantinos; Markowitz, Victor; Szeto, Ernest; Ivanova, Natalia; Mikhailova, Natalia; Pagani, Ioanna; Pati, Amrita; Goodwin, Lynne; Woyke, Tanja; Kyrpides, Nikos

    2013-12-20

    Rhizobium leguminosarum bv. trifolii WSM2012 (syn. MAR1468) is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an ineffective root nodule recovered from the roots of the annual clover Trifolium rueppellianum Fresen growing in Ethiopia. WSM2012 has a narrow, specialized host range for N2-fixation. Here we describe the features of R. leguminosarum bv. trifolii strain WSM2012, together with genome sequence information and annotation. The 7,180,565 bp high-quality-draft genome is arranged into 6 scaffolds of 68 contigs, contains 7,080 protein-coding genes and 86 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program.

  17. 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

  18. Mutations inducing an active-site aperture in Rhizobium sp. sucrose isomerase confer hydrolytic activity.

    PubMed

    Lipski, Alexandra; Watzlawick, Hildegard; Ravaud, Stéphanie; Robert, Xavier; Rhimi, Moez; Haser, Richard; Mattes, Ralf; Aghajari, Nushin

    2013-02-01

    Sucrose isomerase is an enzyme that catalyzes the production of sucrose isomers of high biotechnological and pharmaceutical interest. Owing to the complexity of the chemical synthesis of these isomers, isomaltulose and trehalulose, enzymatic conversion remains the preferred method for obtaining these products. Depending on the microbial source, the ratio of the sucrose-isomer products varies significantly. In studies aimed at understanding and explaining the underlying molecular mechanisms of these reactions, mutations obtained using a random-mutagenesis approach displayed a major hydrolytic activity. Two of these variants, R284C and F164L, of sucrose isomerase from Rhizobium sp. were therefore crystallized and their crystal structures were determined. The three-dimensional structures of these mutants allowed the identification of the molecular determinants that favour hydrolytic activity compared with transferase activity. Substantial conformational changes resulting in an active-site opening were observed, as were changes in the pattern of water molecules bordering the active-site region.

  19. Biological behavior of plasmid in Rhizobium sp. strain S25 from Tephrosia candida.

    PubMed

    Zou, X; Feng, X L; Chen, W X; Li, F D

    1998-09-01

    Rhizobium sp. strain S25 was isolated from the nodule on Tephrosia candida in Hainan Province, China. The strain showed high stress tolerance. The plasmid profile of strain S25, examined by the Eckhardt procedure, indicated that the strain harbors only one plasmid with an estimated size of 150 kb. The plasmid was shown to carry nod and nif genes by hybridization with probes of nodABC and nifHDK genes. Plasmid curing was carried out using the Bacillus subtilis sacB to generate derivatives of strain S25. In comparison with the parent strain S25, the cured derivative lost its ability to nodulate the host plant. Loss of the plasmid reduced significantly the strain's tolerance to acid, nitrous, and multiple antibiotics. The properties of the cured strain also indicated that the plasmid was involved in carbon and nitrogen metabolism. Reintroduction of the plasmid from S25 in the cured derivative restored its original biological phenotypes.

  20. Novel high- and low-copy stable cosmids for use in Agrobacterium and Rhizobium.

    PubMed

    Gallie, D R; Novak, S; Kado, C I

    1985-09-01

    Presented are a set of cosmids based on the unit copy Agrobacterium plasmid, pTAR, and the high-copy-number mutant plasmid, pUCD500, of pTiC58. The addition of a par function derived from pTAR to the vectors allowed them to be stably maintained throughout the cell population in the absence of selective pressure. These vectors, designed for Agrobacterium and Rhizobium, also work in Escherichia coli. The vectors can be cotransferred to Rhizobiaceae from E. coli with the helper plasmid, pRK2013. The pTiC58 origin containing vectors, pUCD1000 and pUCD1001 were found to be incompatible with a 250-kb plasmid harbored by R. meliloti RM102Z1. RM102Z1(pUCD1000) was still capable of nodulating roots in alfalfa.

  1. Biodegradation of hazardous triphenylmethane dye methyl violet by Rhizobium radiobacter (MTCC 8161).

    PubMed

    Parshetti, Ganesh; Saratale, Ganesh; Telke, Amar; Govindwar, Sanjay

    2009-09-01

    Rhizobium radiobacter MTCC 8161 completely decolorized methyl violet (10 mg l(-1)) within 8 h both at static and shaking conditions. The decolorization time increased with increasing dye concentration. The effect of different carbon and nitrogen sources on the decolorization of methyl violet was studied. The maximum decolorization was observed in the presence of sucrose (1%) and urea (1%). UV-Visible, HPLC and FTIR analysis of extracted products confirmed biodegradation of methyl violet. The significant increase in the activities of lignin peroxidase and aminopyrine N-demethylase in the cells obtained after decolorization indicated involvement of these enzymes in the decolorization process. In addition to methyl violet, this strain also shows an ability to decolorize various industrial dyes, (red HE7B, yellow 4G, blue 2B, navy blue HE22, red M5B and red HE3B).

  2. [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.

  3. 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 PAGES

    Natarajan, Padmaja; Punta, Marco; Kumar, Abhinav; ...

    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.

  4. Host Plant Cultivar Effects on Hydrogen Evolution by Rhizobium leguminosarum1

    PubMed Central

    Bedmar, Eulogio J.; Edie, Scott A.; Phillips, Donald A.

    1983-01-01

    The effect of host plant cultivar on H2 evolution by root nodules was examined in symbioses between Pisum sativum L. and selected strains of Rhizobium leguminosarum. Hydrogen evolution from root nodules containing Rhizobium represents the sum of H2 produced by the nitrogenase enzyme complex and H2 oxidized by any uptake hydrogenase present in those bacterial cells. Relative efficiency (RE) calculated as RE = 1 − (H2 evolved in air/C2 H2 reduced) did not vary significantly among `Feltham First,' `Alaska,' and `JI1205' peas inoculated with R. leguminosarum strain 300, which lacks uptake hydrogenase activity (Hup−). That observation suggests that the three host cultivars had no effect on H2 production by nitrogenase. However, RE of strain 128C53 was significantly (P ≤ 0.05) greater in symbiosis with cultivar JI1205 than in root nodules of Feltham First. At a similar rate of C2H2 reduction on a whole-plant basis, nearly 24 times more H2 was evolved from the Feltham First/128C53 symbiosis than from the JI1205/128C53 association. Root nodules from the Alaska/128C53 symbiosis had an intermediate RE over the entire study period, which extended from 21 to 36 days after planting. Direct assays of uptake hydrogenase by two methods showed significant (P ≤ 0.05) host cultivar effects on H2 uptake capacity of both strain 128C53 and the genetically related strain 3960. The 3H2 incorporation assay showed that strains 128C53 and 3960 in symbiosis with Feltham First had about 10% of the uptake hydrogenase activity measured in root nodules of Alaska or JI1205. These data are the first demonstration of significant host plant effects on rhizobial uptake hydrogenase in a single plant species. PMID:16663112

  5. IMMUNE DIFFUSION ANALYSIS OF THE EXTRACELLULAR SOLUBLE ANTIGENS OF TWO STRAINS OF RHIZOBIUM MELILOTI

    PubMed Central

    Dudman, W. F.

    1964-01-01

    Dudman, W. F. (Commonwealth Scientific and Industrial Research Organization, Canberra, Australia). Immune diffusion analysis of the extracellular soluble antigens of two strains of Rhizobium meliloti. J. Bacteriol. 88:782–794. 1964.—Immune diffusion techniques applied to cultures of two strains of Rhizobium meliloti grown in liquid defined medium showed the presence of multiple antigens. Improved resolution of precipitin patterns was obtained with concentrated antigens separated from the cultures as the extracellular soluble fraction or as suspensions of washed cells. The extracellular fraction contained the same diffusible antigens as the washed cells, but additional antigens were found in the cells after ultrasonic disruption. The extracellular soluble antigens were shown by analysis to contain polysaccharide and protein components. In immune diffusion systems, they gave rise to three groups of precipitin bands, two of which were characterized as polysaccharides by their susceptibility to periodate oxidation, and the third as protein by its lability to heat. All the extracellular antigens of both strains were shared except a fast-diffusing polysaccharide, which was specific for each strain. Despite the sharing of all but one of their antigens, cells of these strains showed only a low degree of cross-agglutination, suggesting that their surfaces are dominated by the specific polysaccharide. No differences could be found in the composition of the polysaccharides in the unfractionated extracellular antigens of the two strains, the main components of which were glucose (66%) and galactose (12%) in the presence of several other unidentified sugars in smaller amounts. The pattern of precipitin bands produced in immune diffusion systems by the extracellular soluble fraction could be changed by altering the cultural conditions. Images PMID:14208519

  6. Expression cloning and biochemical characterization of a Rhizobium leguminosarum lipid A 1-phosphatase.

    PubMed

    Karbarz, Mark J; Kalb, Suzanne R; Cotter, Robert J; Raetz, Christian R H

    2003-10-10

    Lipid A of Rhizobium leguminosarum, a nitrogen-fixing plant endosymbiont, displays several significant structural differences when compared with Escherichia coli. An especially striking feature of R. leguminosarum lipid A is that it lacks both the 1- and 4'-phosphate groups. Distinct lipid A phosphatases that attack either the 1 or the 4' positions have previously been identified in extracts of R. leguminosarum and Rhizobium etli but not Sinorhizobium meliloti or E. coli. Here we describe the identification of a hybrid cosmid (pMJK-1) containing a 25-kb R. leguminosarum 3841 DNA insert that directs the overexpression of the lipid A 1-phosphatase. Transfer of pMJK-1 into S. meliloti 1021 results in heterologous expression of 1-phosphatase activity, which is normally absent in extracts of strain 1021, and confers resistance to polymyxin. Sequencing of a 7-kb DNA fragment derived from the insert of pMJK-1 revealed the presence of a lipid phosphatase ortholog (designated LpxE). Expression of lpxE in E. coli behind the T7lac promoter results in the appearance of robust 1-phosphatase activity, which is normally absent in E. coli membranes. Matrix-assisted laser-desorption/time of flight and radiochemical analysis of the product generated in vitro from the model substrate lipid IVA confirms the selective removal of the 1-phosphate group. These findings show that lpxE is the structural gene for the 1-phosphatase. The availability of lpxE may facilitate the re-engineering of lipid A structures in diverse Gram-negative bacteria and allow assessment of the role of the 1-phosphatase in R. leguminosarum symbiosis with plants. Possible orthologs of LpxE are present in some intracellular human pathogens, including Francisella tularensis, Brucella melitensis, and Legionella pneumophila.

  7. Genomic lineages of Rhizobium etli revealed by the extent of nucleotide polymorphisms and low recombination

    PubMed Central

    2011-01-01

    Background Most of the DNA variations found in bacterial species are in the form of single nucleotide polymorphisms (SNPs), but there is some debate regarding how much of this variation comes from mutation versus recombination. The nitrogen-fixing symbiotic bacteria Rhizobium etli is highly variable in both genomic structure and gene content. However, no previous report has provided a detailed genomic analysis of this variation at nucleotide level or the role of recombination in generating diversity in this bacterium. Here, we compared draft genomic sequences versus complete genomic sequences to obtain reliable measures of genetic diversity and then estimated the role of recombination in the generation of genomic diversity among Rhizobium etli. Results We identified high levels of DNA polymorphism in R. etli, and found that there was an average divergence of 4% to 6% among the tested strain pairs. DNA recombination events were estimated to affect 3% to 10% of the genomic sample analyzed. In most instances, the nucleotide diversity (π) was greater in DNA segments with recombinant events than in non-recombinant segments. However, this degree of recombination was not sufficiently large to disrupt the congruence of the phylogenetic trees, and further evaluation of recombination in strains quartets indicated that the recombination levels in this species are proportionally low. Conclusion Our data suggest that R. etli is a species composed of separated lineages with low homologous recombination among the strains. Horizontal gene transfer, particularly via the symbiotic plasmid characteristic of this species, seems to play an important role in diversity but the lineages maintain their evolutionary cohesiveness. PMID:22004448

  8. Gene Products of the hupGHIJ Operon Are Involved in Maturation of the Iron-Sulfur Subunit of the [NiFe] Hydrogenase from Rhizobium leguminosarum bv. viciae

    PubMed Central

    Manyani, Hamid; Rey, Luis; Palacios, José M.; Imperial, Juan; Ruiz-Argüeso, Tomás

    2005-01-01

    In the present study, we investigate the functions of the hupGHIJ operon in the synthesis of an active [NiFe] hydrogenase in the legume endosymbiont Rhizobium leguminosarum bv. viciae. These genes are clustered with 14 other genes including the hydrogenase structural genes hupSL. A set of isogenic mutants with in-frame deletions (ΔhupG, ΔhupH, ΔhupI, and ΔhupJ) was generated and tested for hydrogenase activity in cultures grown at different oxygen concentrations (0.2 to 2.0%) and in symbiosis with peas. In free-living cultures, deletions in these genes severely reduced hydrogenase activity. The ΔhupH mutant was totally devoid of hydrogenase activity at any of the O2 concentration tested, whereas the requirement of hupGIJ for hydrogenase activity varied with the O2 concentration, being more crucial at higher pO2. Pea bacteroids from the mutant strains affected in hupH, hupI, and hupJ exhibited reduced (20 to 50%) rates of hydrogenase activity compared to the wild type, whereas rates were not affected in the ΔhupG mutant. Immunoblot experiments with HupL- and HupS-specific antisera showed that free-living cultures from ΔhupH, ΔhupI, and ΔhupJ mutants synthesized a fully processed mature HupL protein and accumulated an unprocessed form of HupS (pre-HupS). Both the mature HupL and the pre-HupS forms were located in the cytoplasmic fraction of cultures from the ΔhupH mutant. Affinity chromatography experiments revealed that cytoplasmic pre-HupS binds to the HupH protein before the pre-HupS-HupL complex is formed. From these results we propose that hupGHIJ gene products are involved in the maturation of the HupS hydrogenase subunit. PMID:16199572

  9. 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.

  10. 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.

  11. Growth and yield of groundnut (Arachis hypogaea L.) as influenced by weed management practices and Rhizobium inoculation.

    PubMed

    Jhala, A; Rathod, P H; Patel, K C; Van Damme, P

    2005-01-01

    Groundnut (Arachis hypogaea L.) productivity in India is low, because of many problems beset in its cultivation. One of the serious problems are weeds. Groundnut yield losses due to weeds have been estimated as high as 24 to 70 percent. This has created a scope for using herbicides in groundnut crop. A field investigation was carried out during kharif (rainy) season of 2001-2002 on a sandy loam soil at College Agronomy Farm, B.A. College of Agriculture, Gujarat Agricultural University, Anand, India to study the effect of weed management practices and Rhizobium inoculation on growth and yield of groundnut (Arachis hypogaea L.). Ten weed control treatments, comprising four treatments of sole application of fluchloralin, pendimethalin, butachlor and metolachlor, respectively each applied at 1.0 kg ha(-1); four treatments comprising of an application of the same herbicides at the same levels coupled with one hand weeding at 30 DAS; one weed-free treatment (hand weedings at 15, 30, 45 DAS); and one unweeded control. All 10 treatmets were combined with and without Rhizobium inoculation (i.e. a total of 20 treatment combinations) under a factorial randomized complete block design (FRBD) with four replications. Minimum weed dry matter accumulation (70 kg/ha) with higher weed control efficiency (90.70%) was recorded under an integrated method i.e. pendimethalin at 1.0 kg ha(-1) + hand weeding at 30 DAS, which also resulted in maximum pod yield (1773.50 kg ha(-1)). This treatment was comparable to fluchloralin applied at 1.0 kg ha(-1) combined with hand- weeding at 30 DAS. Weedy conditions in the unweeded control treatment reduced pod yield by 29.90-35.95% as compared to integrated method. Significantly higher pod yield was obtained with Rhizobium inoculation than the mean value of all treatments without inoculation. For most agronomical parameters examined, Rhizobium inoculation and weed control treatments were independent in their effect.

  12. Characterization of Rhizobium naphthalenivorans sp. nov. with special emphasis on aromatic compound degradation and multilocus sequence analysis of housekeeping genes.

    PubMed

    Kaiya, Shinichi; Rubaba, Owen; Yoshida, Naoko; Yamada, Takeshi; Hiraishi, Akira

    2012-01-01

    Three strains of aerobic chemoorganotrophic naphthalene-degrading bacteria (designated TSY03b(T), TSY04, and TSW01) isolated from sediment of a polychlorinated-dioxin-transforming microcosm were characterized. These strains had Gram-negative-stained, rod-shaped cells measuring 0.6‒0.9 μm in width and 1.2‒3.0 μm in length and were motile by means of peritrichous flagella. Naphthalene was utilized as the sole carbon and energy source, and the transcription of a putative aromatic-ring hydroxylating gene was inducible by naphthalene. The major component of cellular fatty acids was summed feature 8 (C18:1ω7c and/or C18:1ω6c), and significant proportions of C18:0 and C19:0 cyclo ω8cis were also found. The major respiratory quinone was ubiquinone-10. The G+C content of the DNA was 60.3‒60.9 mol%. Phylogenetic analyses by studying sequence information on the housekeeping atpD, dnaK, glnII, gyrB, and recA genes as well as on 16S rRNA genes and the 16S-23S rDNA internal transcribed spacer region revealed that the strains grouped with members of the genus Rhizobium, with Rhizobium selenitireducens as their closest relative but formed a distinct lineage at the species level. This was confirmed by genomic DNA-DNA hybridization studies. These phenotypic, genotypic, and phylogenetic data strongly suggest that our isolates should be classified under a novel species of the genus Rhizobium. Thus, we propose the name Rhizobium naphthalenivorans sp. nov. to accommodate the novel isolates. The type strain is TSY03b(T) (= NBRC 107585T = KCTC 23252T).

  13. Structure-function analysis of nod factor-induced root hair calcium spiking in Rhizobium-legume symbiosis.

    PubMed

    Wais, Rebecca J; Keating, David H; Long, Sharon R

    2002-05-01

    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.

  14. 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.

  15. Sulphation of Rhizobium sp. NGR234 Nod factors is dependent on noeE, a new host-specificity gene.

    PubMed

    Hanin, M; Jabbouri, S; Quesada-Vincens, D; Freiberg, C; Perret, X; Promé, J C; Broughton, W J; Fellay, R

    1997-06-01

    Rhizobia secrete specific lipo-chitooligosaccharide signals (LCOs) called Nod factors that are required for infection and nodulation of legumes. In Rhizobium sp. NGR234, the reducing N-acetyl-D-glucosamine of LCOs is substituted at C6 with 2-O-methyl-L-fucose which can be acetylated or sulphated. We identified a flavonoid-inducible locus on the symbiotic plasmid pNGR234a that contains a new nodulation gene, noeE, which is required for the sulphation of NGR234 Nod factors (NodNGR). noeE was identified by conjugation into the closely related Rhizobium fredii strain USDA257, which produces fucosylated but non-sulphated Nod factors (NodUSDA). R. fredii transconjugants producing sulphated LCOs acquire the capacity to nodulate Calopogonium caeruleum. Furthermore, mutation of noeE (NGRdelta noeE) abolishes the production of sulphated LCOs and prevents nodulation of Pachyrhizus tuberosus. The sulphotransferase activity linked to NoeE is specific for fucose. In contrast, the sulphotransferase NodH of Rhizobium meliloti seems to be less specific than NoeE, because its introduction into NGRdelta noeE leads to the production of a mixture of LCOs that are sulphated on C6 of the reducing terminus and sulphated on the 2-O-methylfucose residue. Together, these findings show that noeE is a host-specificity gene which probably encodes a fucose-specific sulphotransferase.