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At least 19 recordsLinked to original sources
PubMed2006

Zoogloea oryzae sp. nov., a nitrogen-fixing bacterium isolated from rice paddy soil, and reclassification of the strain ATCC 19623 as Crabtreella saccharophila gen. nov., sp. nov.

Two strains of free-living diazotrophs isolated from soil from a rice paddy field were characterized by using a polyphasic approach. The novel strains, A-7T and A-4, were found to be very closely related, with 99.9% 16S rRNA gene sequence similarity and a DNA-DNA hybridization value of 89.5%, suggesting that they represent a single species. 16S rRNA gene sequence analyses indicated that the two strains fell within the Zoogloea lineage, with less than 96.7 % sequence similarity to other Zoogloea species. Chemotaxonomic characteristics of the novel strains, including DNA G + C content (65.1 mol%), the major quinone system (Q-8), predominant fatty acids (16:1omega7c and 16:0) and major hydroxy fatty acids (3-OH 10:0 and 3-OH 12:0), are similar to those of the genus Zoogloea. The novel strains showed positive results for floc formation which is accepted as confirmatory for species of the genus Zoogloea. However, the novel strains can be distinguished from the other species of Zoogloea by physiological characteristics. The name Zoogloea oryzae sp. nov. is therefore proposed for the novel strains with strain A-7T (= IAM 15218T = CCTCC AB 2052005T) as the type strain. Phylogenetic and chemotaxonomic analyses indicate that strain ATCC 19623, designated as a reference strain of Zoogloea ramigera, does not belong to the genus Zoogloea but to a new genus of Alphaproteobacteria. The name Crabtreella saccharophila gen. nov., sp. nov. is proposed for strain ATCC 19623T (= IAM 12669T).

Alphaproteobacteria↗
PubMed1967

Occurrence of zoogloea colonies and protozoans at different stages of sewage purification.

The presence of fingered branch-bearing Zoogloea has been noted on a number of occasions in the Baroda Sewage Disposal Works. Samples of raw sewage, the effluent from the continuous flow settling basin, the raw sludge, the floating scum in the settling basin, the final secondary digested sludge, and the supernatant liquid from the secondary digester were kept without any disturbance in 1-liter Pyrex glass beakers, which were loosely covered with petri dishes. Scum was formed on the surface within 48 hr in all the samples, and fingered Zoogloea colonies resembling the pure culture of Zoogloea ramigera reported by Crabtree et al. (5) were found in all except the final secondary digested sludge and the supernatant liquid from the secondary digester. It is not known whether the Zoogloea colonies discovered in the above cases are the same as or different from the typical Zoogloea ramigera of activated sludge, and whether they are slime-forming or flocculent types of bacteria. In any case, they seem to be different in their ecological status and in the nature of the accompanying protozoans from the typical Zoogloea ramigera. The reasons for the absence of zoogloeas in two of the samples are unknown.

Journal Article↗
PubMed1992

Isoprenoid quinones and fatty acids of Zoogloea.

Nine Zoogloea strains including the type strain of Z. ramigera (IAM 12136 = ATCC 19544 = N.C. Dondero 106) and newly isolated strains were investigated for isoprenoid quinone composition and whole-cell fatty acid profiles. Seven of the tested strains, having phenotypic properties typical of Zoogloea, were characterized by their production of both ubiquinone-8 and rhodoquinone-8 as major quinones, whereas the remaining two strains, Z. ramigera IAM 12669 (= K. Crabtree I-16-M) and IAM 12670 (= P.R. Dugan 115), formed ubiquinone-10 and ubiquinone-8, respectively, as the sole quinone. All rhodoquinone-producing strains contained palmitoleic acid and 3-hydroxy-decanoic acid as the major components of nonpolar and hydroxylated fatty acids, respectively. Marked differences were noted in the fatty acid composition between the strains with and without rhodoquinones. The chemotaxonomic data suggested that the rhodoquinone-lacking strains should be excluded from the genus Zoogloea. Since there have been no reliable taxonomic tools for Zoogloea, rhodoquinone analysis may provide a new criterion of great promise for identifying Zoogloea strains.

Chromatography, High Pressure Liquid↗
PubMed1993

Molecular systematics of the genus Zoogloea and emendation of the genus.

Phylogenetic relationships among strains of Zoogloea and related taxa were determined by 16S rDNA sequencing and genomic DNA hybridization techniques. The 16S rRNA gene was amplified by the polymerase chain reaction with a pair of eubacterial consensus primers and sequenced directly by using an automated fluorescent DNA sequencer. Sequence comparisons and distance matrix tree analysis revealed that Zoogloea ramigera IAM 12136 (= N. C. Dondero 106, type strain) and Zoogloea sp. ATCC 19324 formed a lineage with Rhodocyclus purpureus in the beta subclass of Proteobacteria. Z. ramigera IAM 12670 (= P. R. Dugan 115) was shown to belong to another cluster with Alcaligenes eutrophus and Pseudomonas cepacia in the beta subclass. In contrast, Z. ramigera IAM 12669 (= K. Crabtree I-16-M) proved to be a member of the alpha subclass of the Proteobacteria, closely related to Agrobacterium tumefaciens. Genomic DNA hybridization studies also showed that there is genetic diversity among the strains currently designated Z. ramigera, but typical Zoogloea strains, characterized by their production of rhodoquinones, are highly related to each other and can be regarded as a single species. On the basis of the molecular data, together with the early phenotypic and chemotaxonomic information, we have emended the generic description of Zoogloea.

Base Composition↗
PubMed2001

Immunological methods for the study of Zoogloea strains in natural environments.

Since Zoogloea ramigera has been considered to be important in aerobic wastewater treatment, we have evaluated several methods for detecting and enumerating Z. ramigera in water and wastewater samples. Indirect immunoassay methods for the detection of Zoogloea strains were developed using polyclonal antibodies against the cells or the isolated exocellular polymer (EP) of the neotype Zoogloea ramigera strain 106 (ATCC 19544). The primary antibodies reacted with the cells and the exopolymer associated with finger-like zoogloeal projections, but not with other bacteria from natural samples. These antibodies allowed detection of Z. ramigera in environmental samples. Scanning electron microscopy (SEM) was used to show that the cells and the exocellular polymer of naturally occurring zoogloeal projections are antigenically and structurally related to those of Z. ramigera 106. Both immunological procedures and probes complementary to regions on the 16S rRNA could detect Z. ramigera in natural samples but the immunological procedures were easier to use. RT-PCR was also used to detect Z. ramigera in natural samples. These methods were also used to identify Z. ramigera in biofilms that developed over wastewater samples as part of an MPN procedure that was used to quantitate Z. ramigera at different stages of the wastewater treatment process and in different lakes. Z. ramigera could be found in all stages of wastewa ter treatment processes, from raw wastewater to chlorinated effluent, The highest concentration of Z. ramigera was found in the mixed liquor stage of the a wastewater treatment plant. Additionally, Z. ramigera was found in all eutrophic and mesotrophic lakes and in some oligotrophic lakes.

Biofilms↗
PubMed1972

Use of aromatic compounds for growth and isolation of Zoogloea.

Nine Zoogloea strains, were examined for their ability to utilize 35 aromatic compounds. Benzoate, m-toluate, and p-toluate, as well as phenol, o-cresol, m-cresol, and p-cresol, were utilized by eight strains. These strains exhibited meta cleavage of catechol and of methyl-substituted catechols. With the exception of L-tyrosine, none of the aromatic compounds tested supported growth of Z. ramigera ATCC 19623. A medium containing sodium m-toluate was used to isolate 37 zoogloea-forming bacteria from various polluted environments. The isolates were identified as strains of Zoogloea.

Bacteriological Techniques↗
PubMed1975

Fluorescent-antibody study of natural finger-like zoogloeae.

Fluorescent-antibody techniques using Zoogloea ramigera 106 antiserum were used to study fresh activated sludge flocs and finger-like zoogloeae in the microbial film that developed over stored samples of activated sludge. Few cells in fresh activated sludge reacted positively with the fluorescein-labeled antiserum. Finger-like zoogloeae containing reactive cells were readily observed in the microbial film layer over stored activated sludge. Certain of the naturel finger-like projections were entirely composed of cells that reacted positively to the labeled Z. ramigera 106 antiserum, whereas other projections were devoid of reactive cells.

Antigens, Bacterial↗
PubMed2006

Shinella granuli gen. nov., sp. nov., and proposal of the reclassification of Zoogloea ramigera ATCC 19623 as Shinella zoogloeoides sp. nov.

The taxonomic position of a novel bacterial strain, Ch06T, isolated from an upflow anaerobic sludge blanket reactor was determined. Strain Ch06T was Gram-negative, aerobic, motile and oxidase- and catalase-positive. A comparative 16S rRNA gene sequence analysis showed a clear affiliation of strain Ch06T to the Alphaproteobacteria and it was most closely related to Zoogloea ramigera ATCC 19623 and Mycoplana dimorpha IAM 13154T (97.9 and 96.3% sequence similarity, respectively). The major respiratory quinone was Q-10 and the predominant fatty acids were C16:0, 3-OH C16:0, C18:0, C19:0 cyclo omega8c and summed feature 7 (C18:1omega7c/omega9t/omega12t, C18:1omega7c/omega9c/omega12t). On the basis of phenotypic, chemotaxonomic and phylogenetic characteristics, the novel isolate was assigned to a new genus, Shinella gen. nov., as Shinella granuli gen. nov., sp. nov. (type strain Ch06T=KCTC 12237T=JCM 13254T). It is proposed that Zoogloea ramigera ATCC 19623 is reclassified into the novel genus Shinella as Shinella zoogloeoides sp. nov. (type strain ATCC 19623T=IAM 12669T=I-16-MT).

Alphaproteobacteria↗
PubMed1995

The abundance of Zoogloea ramigera in sewage treatment plants.

Zoogloea ramigera has long been considered the typical activated sludge bacterium responsible for the formation of activated sludge flocs. On the basis of the results of a comparative sequence analysis, we designed three oligonucleotide probes complementary to characteristic regions of the 16S rRNAs of Z. ramigera ATCC 19544T (T = type strain) and two misclassified strains, Z. ramigera ATCC 25935 and ATCC 19623. Dissociation temperatures were determined, and probe specificities, as well as the potential of probes for whole-cell hybridization, were evaluated by using numerous reference organisms. Several activated sludge samples were examined with these probes by using both the in situ and dot blot hybridization methods. Only the type strain probe hybridized to cells that accumulated in the typical branched gelatinous matrices, the so-called Zoogloea fingers. This probe revealed cells in most of the activated sludge samples studied. We found that relatively high levels of Z. ramigera cells (up to approximately 10% of the total number of cells) and typical morphology tended to be linked to overloading of sewage plants. The probe directed to rejected type strain Z. ramigera ATCC 19623 bound to only a few cells. Cells that reacted with the probe complementary to Z. ramigera ATCC 25935, which was originally isolated from a trickling filter, were not observed in activated sludge.

Base Sequence↗
PubMed1982

Synergistic Interaction Between Anabaena and Zoogloea spp. in Carbon Dioxide-Limited Continuous Cultures.

Flocs consisting of Anabaena and Zoogloea spp. were used as a model system for the study of planktonic phototroph-heterotroph interactions. In CO(2)-limited continuous culture (3.2 mumol of NaHCO(3) liter h, 1.5 mumol of glucose liter h, pH 8.5, D = 0.026 h), the biomass of the phototroph increased 8.6-fold due to association. However, direct CO(2) exchange accounted for only a 3.8-fold increase. When the glucose supply rate was increased to 7.5 mumol liter h, there was a 26-fold increase in biomass. When CO(2) was supplied in excess, there was no difference due to association. In batch culture, using the same medium, the specific growth rate was 0.029 h for the phototroph alone and 0.047 h for the phototroph in association with the heterotroph. The stimulatory effect of the heterotroph was found only under CO(2)-limiting conditions and was directly related to the concentration of organic matter supplied in the medium. Both the biomass and the growth rate of the Anabaena sp. were increased by association with the Zoogloea sp. Thus, dissolved organic matter may substitute for CO(2) to maximize both growth rate and biomass production by phototrophs when heterotrophic bacteria are present.

Journal Article↗
PubMed1968

Identification of Zoogloea species and the relationship to zoogloeal matrix and floc formation.

Three floc-forming, gram-negative, polarly flagellated rods were isolated and characterized. Our isolates were compared to four similar floc-forming organisms previously isolated in another laboratory and classified as two species of Zoogloea, one of Pseudomonas, and as one unidentified gram-negative rod. Possession of zoogloeal matrix or flocculent growth habit was examined in relation to growth and biochemical patterns of the bacteria. A possible relationship of Zoogloea to other gelatinous matrix-producing bacteria is also discussed.

Bacteria↗
PubMed2000

Crystallographic analysis of the reaction pathway of Zoogloea ramigera biosynthetic thiolase.

Biosynthetic thiolases catalyze the biological Claisen condensation of two acetyl-CoA molecules to form acetoacetyl-CoA. This is one of the fundamental categories of carbon skeletal assembly patterns in biological systems and is the first step in many biosynthetic pathways including those which generate cholesterol, steroid hormones and ketone body energy storage molecules. High resolution crystal structures of the tetrameric biosynthetic thiolase from Zoogloea ramigera were determined (i) in the absence of active site ligands, (ii) in the presence of CoA, and (iii) from protein crystals which were flash frozen after a short soak with acetyl-CoA, the enzyme's substrate in the biosynthetic reaction. In the latter structure, a reaction intermediate was trapped: the enzyme was found to be acetylated at Cys89 and a molecule of acetyl-CoA was bound in the active site pocket. A comparison of the three new structures and the two previously published thiolase structures reveals that small adjustments in the conformation of the acetylated Cys89 side-chain allow CoA and acetyl-CoA to adopt identical modes of binding. The proximity of the acetyl moiety of acetyl-CoA to the sulfur atom of Cys378 supports the hypothesis that Cys378 is important for proton exchange in both steps of the reaction. The thioester oxygen atom of the acetylated enzyme points into an oxyanion hole formed by the nitrogen atoms of Cys89 and Gly380, thus facilitating the condensation reaction. The interaction between the thioester oxygen atom of acetyl-CoA and His348 assists the condensation step of catalysis by stabilizing a negative charge on the thioester oxygen atom. Our structure of acetyl-CoA bound to thiolase also highlights the importance in catalysis of a hydrogen bonding network between Cys89 and Cys378, which includes the thioester oxygen atom of acetyl-CoA, and extends from the catalytic site through the enzyme to the opposite molecular surface. This hydrogen bonding network is different in yeast degradative thiolase, indicating that the catalytic properties of each enzyme may be modulated by differences in their hydrogen bonding networks.

Acetyl Coenzyme A↗
PubMed1978

Purification and properties of beta-ketothiolase from Zoogloea ramigera.

beta-Ketothiolase from Zoogloea ramigera I-16-M was purified 140-fold to electrophoretic homogeneity. The bacterium appeared to contain a single isoenzyme of beta-ketothiolase with a molecular weight of 190 000, as determined by Sephadex G-200 gel filtration. The monomer molecular weight was 44 000, as estimated by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. The native enzyme thus appeared to be a tetramer with identical subunits. The enzyme showed a pH optimum of 7.5 in the condensation reaction, and 8.5 in the thiolysis reaction. The enzyme employed a Bi Bi ping pong mechanism for the forward thiolysis reaction. The apparent Km value for acetoacetyl coenzyme A in the thiolysis reaction was 10 micron, and that for coenzyme A was 8.5 micron. The apparent Km value for acetyl coenzyme A in the condensation reaction was 0.33 mM. The condensation reaction was inhibited by coenzyme A concentrations lower than 0.1 mM. The enzyme was stable in the presence of dithiothreitol and other SH-compounds, but was strongly inhibited by 0.4 mM p-chloromercuribenzoate.

Acetyl Coenzyme A↗
PubMed1988

Oxygen and nitrate reduction kinetics of a nonflocculating strain of Zoogloea ramigera.

The oxygen and nitrate reduction kinetics of a nonflocculating strain of Zoogloea ramigera were determined. Axenic, nitrate-reducing bacterial suspensions were acclimated to various oxygen levels in a chemostat while measuring nitrate reduction in the presence of high ammonium nitrogen concentrations. Significant nitrate reduction was observed at oxygen concentrations up to 8 mg L-1. Oxygen consumption was inhibited by oxygen concentrations in excess of 2 mg L-1.

Bacteriological Techniques↗
PubMed1977

An NADP-linked acetoacetyl CoA reductase from Zoogloea ramigera.

Zoogloea ramigera I-16 M was found to contain two stereospecific acetoacetyl CoA reductases; one was NADP+-linked and D(-)-beta-hydroxybutyryl CoA specific and the other was NAD+-linked and L(+)-isomer specific. The NADP+-linked enzyme, purified approximately 150-fold, had a pH optimum for the reduction of acetoacetyl CoA at 8.1, but no definite pH optimum for the oxidation for beta-hydroxybutyryl CoA. The apparent Michaelis constants for acetoacetyl CoA and NADPH were 8.3 and 21 micrometer, respectively. The enzyme was markedly inhibited by acetoacetyl CoA at concentrations higher than 10 micrometer. The incorporation of [1-14C]acetyl CoA into poly-beta-hydroxybutyrate (PHB) by bacterial crude extract (containing beta-ketothiolase, acetoacetyl CoA reductases, enoyl CoA hydratases and PHB synthases) or by a system reconstituted from purified preparations of beta-ketothiolase, acetoacetyl CoA reductase and PHB synthase, was observed only in the presence of NADPH, but not NADH. Among various enzymes involved in PHB metabolism, only the specific activity of glucose 6-phosphate dehydrogenase was elevated 5-fold within 2 h after the addition of glucose to the cells grown in the basal medium. These findings suggest that, in Z. ramigera I-16M, acetoacetyl CoA is directly reduced to D(-)-beta-hydroxybutyryl CoA by the NADP+-dependent reductase, and PHB synthesis is at least partially controled by NADPH availability through glucose 6-phosphate dehydrogenase.

Acetoacetates↗
PubMed1976

Enzymatic synthesis of poly-beta-hydroxybutyrate in Zoogloea ramigera.

The enzyme activity synthesizing poly-beta-hydroxybutyrate (PHB) was mainly localized in the PHB-containing particulate fraction of Zoogloea ramigera I-16-M, when it grew flocculatedly in a medium supplemented with glucose. On the other hand, the enzyme activity remained in the soluble fraction when the bacterium grew dispersedly in a glucose-starved medium. The soluble PHB synthase activity became associated with the particulate fraction as PHB synthesis was initiated on the addition of glucose to the dispersed culture. Conversely, the enzyme activity was released from the PHB-containing granules to the soluble fraction when the flocculated culture was kept incubated without supplementing the medium with glucose. PHB synthase was also incorporated into the newly formed PHB fraction when partially purified soluble PHB synthase was incubated with D(-)-beta-hydroxybutyryl CoA in vitro. Although attempts to solubilize the particulate enzyme were unsuccessful, and the soluble enzyme became extremely unstable in advanced stages of purification, both PHB synthases had the same strict substrate specificity for D(-)-beta-hydroxybutyryl CoA, and showed the same pH optimum at 7.0.

Coenzyme A Ligases↗
PubMed1992

Intracellular degradation of poly(3-hydroxybutyrate) granules of Zoogloea ramigera I-16-M.

Intracellular degradation of poly(3-hydroxybutyrate) (PHB) in bacteria is not yet clear. The properties of the autodigestion of native PHB granules from Zoogloea ramigera I-16-M were examined. The release of D(-)-3-hydroxybutyrate was observed only at pH values higher than about 8.5 and at relatively high ionic strength (optimal concentration 200 mM NaCl). Triton X-100 and diisopropylfluorophosphate inhibited this reaction. Addition of the supernatant fraction of Z. ramigera did not increase the release of D(-)-3-hydroxybutyrate from the native PHB granules. On the other hand, using the protease-treated PHB granules from Alcaligenes eutrophus as a substrate, PHB depolymerase activity was detected in the supernatant fraction of Z. ramigera cells. The soluble PHB depolymerase showed similar properties to the enzyme in the PHB granules. Since PHB depolymerase activity was found in fractions containing D(-)-3-hydroxybutyrate oligomer hydrolase activity, which were separated by DEAE-Toyopearl or by Sephacryl S-100, it is possible that the intracellular PHB depolymerase is identical to the oligomer hydrolase which has been purified already.

Biodegradation, Environmental↗