bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of the Biolog Substrate Utilization System To Identify and Assess Metabolic Variation among Strains of
Xanthomonas campestris
pv. Citri
Authors: Verniere C. , Pruvost O. , Civerolo E. L. , Gambin O. , Jacquemoud-Collet J. P. , Luisetti J.
Published: January 2020

Metabolic fingerprints of 148 strains of
Xanthomonas campestris
pv. citri originating from 24 countries and associated with various forms of citrus bacterial canker disease (CBCD) were obtained by using the Biolog substrate utilization system. Metabolic profiles were used to attempt strain identification. Only 6.8% of the studied strains were correctly identified when the commercial Microlog 2N data base was used alone. When the data base was supplemented with data from 54 strains of
X. campestris
pv. citri (40 CBCD-A strains, 8 CBCD-B strains, and 6 CBCD-C strains) and data from 43 strains of
X. campestris
associated with citrus bacterial spot disease, the percentage of correct identifications was 70%. Thus, it is recommended that users supplement the commercial data base with additional data prior to using the program for identification purposes. The utilization of Tween 40 in conjunction with other tests can help to differentiate strains associated with CBCD and citrus bacterial spot disease. These results confirmed the separation of
X. campestris
pv. citri into different subgroups (strains associated with Asiatic citrus canker [CBCD-A], cancrosis B [CBCD-B], and Mexican lime canker [CBCD-C]). The utilization of
l
-fucose,
d
-galactose, and alaninamide can be used as markers to differentiate strains associated with these groups. A single strain associated with bacteriosis of Mexican lime in Mexico (CBCD-D) was closely similar to CBCD-B strains.
Characterization of the structural gene encoding a copper-containing nitrite reductase and homology of this gene to DNA of other denitrifiers
Authors: Ye R W , Fries M R , Bezborodnikov S G , Averill B A , Tiedje J M
Published: January 2020

A copper-containing nitrite reductase gene (nirU) from Pseudomonas sp. strain G-179 was found in a 1.9-kb EcoRI-BamHI DNA fragment. The coding region contained information for a polypeptide of 379 amino acids. The encoded protein had 78% identity in amino acid sequence to the nitrite reductase purified from Achromobacter cycloclastes. The ligands for type 1 copper- and type 2 copper-binding sites found in A. cycloclastes were also found in Pseudomonas sp. strain G-179, suggesting that these binding sites are conserved. Upstream from the promoter, two putative fnr boxes were found, suggesting that an FNR-like protein may be involved in regulation of the nitrite reductase gene under anaerobic conditions. When the 1.9-kb clone was used to probe Southern blots for similar sequences in DNAs from different denitrifiers, hybridization bands were seen for 15 of 16 denitrifiers known to have nitrite reductase containing copper. Except for Pseudomonas stutzeri JM300, all denitrifiers tested that have nitrite reductases containing heme c,d1 showed no or weak hybridization to this probe. Thus, this structural gene may be useful as a probe to detect denitrifiers with copper-containing nitrite reductases.
Formation and Regeneration of
Methanococcus voltae
Protoplasts
Authors: Patel G. B. , Choquet C. G. , Nash J. H. E. , Sprott G. D.
Published: January 2020

Methanococcus voltae
cells were converted into protoplasts by suspension in anaerobic 0.1 M Tris-HCl buffer containing 0.4 M sucrose and 0.05 M NaCl as osmoprotectants. Protoplast formation was monitored microscopically by observing the conversion of the typical irregularly shaped (uneven peripheries) coccoid whole cells to rounded forms with smooth peripheries. Although the procedure resulted in about 50% lysis of the initial number of cells, the remainder were converted to the rounded form. Analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and electron microscopy of negatively stained cell preparations indicated that the treatment removed the wall layer from whole cells to yield protoplasts. Protoplast regeneration was evaluated by using optimized plating conditions and an anaerobic microplating technique. Between 50 and 63% of the initial number of protoplasts regenerated as colonies on agar medium (35°C, 7 days). The colony and cell morphologies of the regenerated protoplasts were indistinguishable from those of whole cells plated under identical conditions.
Cobalamin-mediated mercury methylation by Desulfovibrio desulfuricans LS
Authors: Choi S C , Bartha R
Published: January 2020

The prominence of sulfate reducers in mercury biomethylation prompted the examination of the methyl carrier and mercury methylation activity of Desulfovibrio desulfuricans LS. There was a low degree of mercury tolerance and a high degree of methylation during fermentative growth; the opposite was true during sulfate reduction. During 2 days of fermentative growth, up to 37% of HgCl2 was methylated at 0.1 micrograms/ml, but only 1.5% was methylated at 10.0 micrograms/ml. Less than 1% of the added HgCl2 was methylated under sulfate-reducing conditions. D. desulfuricans LS radioimmunoassay results were positive for cobalamin. The addition of CoCl2 and benzimidazole to fermentative cultures increased methylation activity. From D. desulfuricans LS grown in the presence of (57)CoCl2, a corrinoid was extracted and purified. High-performance liquid chromatography analysis of the purified extract yielded a single peak with the retention time of cobalamin, and 97% of the (57)Co radioactivity was associated with this peak. Fast atom bombardment and UV and visible spectra of the isolated corrinoid matched those of cobalamin. When methylated with (14)CH3I, the isolated corrinoid methylated Hg(2+) with a 93.9% preservation of (14)C specific activity. We conclude that D. desulfuricans LS methylates mercury via cobalamin (vitamin B12). Under physiological conditions, the enzymatic catalysis of this reaction is likely.
Construction and characterization of heavy metal-resistant haloaromatic-degrading Alcaligenes eutrophus strains
Authors: Springael D , Diels L , Hooyberghs L , Kreps S , Mergeay M
Published: January 2020

Alcaligenes eutrophus strains exhibiting both plasmid-borne heavy metal resistance and haloaromatic-degrading functions were obtained by intraspecific conjugation. The strains which we constructed expressed catabolic and resistance markers together. Degradation of various polychlorinated biphenyl isomers and 2,4-D (2,4-dichlorophenoxyacetic acid) was observed in the presence of 1 mM nickel or 2 mM zinc, provided that the metal resistance determinant was present in the catabolizing strain. Such strains may be useful for decontamination of sites that are polluted with both organic compounds and heavy metals.
Starvation-survival of a p-nitrophenol-degrading bacterium
Authors: Herman D C , Costerton J W
Published: January 2020

An environmental actinomycetes, capable of utilizing p-nitrophenol as its sole carbon and nitrogen source, was starved for an 8-week period and showed no reduction in its ability to biodegrade p-nitrophenol. Microscopic examination revealed that starvation of the bacterium resulted in the fragmentation of filaments into individual cells.
Cloning and characterization of the gene encoding glutamate 1-semialdehyde 2,1-aminomutase, which is involved in delta-aminolevulinic acid synthesis in Propionibacterium freudenreichii
Authors: Murakami K , Hashimoto Y , Murooka Y
Published: January 2020

The gene from Propionibacterium freudenreichii that encodes glutamate 1-semialdehyde 2,1-aminomutase (EC 5.4.3.8), which is involved in the C5 pathway for synthesis of delta-aminolevulinic acid (ALA), a precursor in heme and cobalamin biosynthesis, was cloned onto a multicopy plasmid, pUC18, via complementation of an ALA-deficient mutant (hemL) of Escherichia coli. Subcloning of fragments from the initial 3.3-kb chromosomal fragment allowed the isolation of a 1.9-kb fragment which could complement the hemL mutation. Nucleotide sequence analysis of the 1.9-kb DNA fragment revealed an open reading frame (ORF) that was located downstream from a potential ribosome-binding site. The ORF encoded a polypeptide of 441 amino acid residues, and the deduced molecular mass of this polypeptide is 45,932 Da. A high G+C content (70 mol%) of the codons of the ORF was found and was consistent with the taxonomic features of Propionibacterium species. The amino acid sequence showed a high degree of homology with those of the HemL proteins from other organisms, and a putative binding site for pyridoxal 5'-phosphate was conserved, with the exception of a single substitution of phenylalanine for leucine. These results suggest that ALA is synthesized via the C5 pathway in a producer of vitamin B12, P. freudenreichii.
Benthic Distribution of Sewage Sludge Indicated by
Clostridium perfringens
at a Deep-Ocean Dump Site
Authors: Hill Russell T. , Knight Ivor T. , Anikis Michael S. , Colwell Rita R.
Published: January 2020

Clostridium perfringens
in sediment samples collected at the Deep Water Municipal Sewage Sludge Disposal Site (also called the 106-Mile Site), off the coast of New Jersey, was enumerated. The counts of
C. perfringens
found in sediment samples collected within and to the southwest of the 106-Mile Site were significantly elevated (
P
< 0.01) compared with counts of samples from reference stations of similar depth (2,400 to 2,700 m), topography, and distance from the continental shelf, indicating that the benthic environment was contaminated by sewage dumping at this site. Low counts of
C. perfringens
in sediment samples collected at stations between the base of the continental shelf and the 106-Mile Site indicated that coastal runoff was not a significant source of contamination. Elevated counts were observed for samples up to 92 km to the southwest, whereas low counts were obtained for samples from stations to the east of the 106-Mile Site. This distribution is consistent with previous model predictions of sludge deposition. In areas heavily impacted by sludge dumping,
C. perfringens
counts were generally highest in the top 1 cm of sediment and exceeded 9,000 CFU g (dry weight) of sediment
-1
. The patterns of
C. perfringens
dispersal observed in this study have proved useful for selection of heavily impacted areas and control stations for further ecological evaluation by a multidisciplinary research team.
Comparative study on the production of guar alpha-galactosidase by Saccharomyces cerevisiae SU50B and Hansenula polymorpha 8/2 in continuous cultures
Authors: Giuseppin M L , Almkerk J W , Heistek J C , Verrips C T
Published: January 2020

Saccharomyces cerevisiae SU50B and Hansenula polymorpha 8/2, both carrying a multicopy integrated guar alpha-galactosidase, have been cultivated in continuous cultures, using various mixtures of carbon sources and cultivation conditions. Both S. cerevisiae SU50B and H. polymorpha 8/2 are stable and produce high levels of extracellular alpha-galactosidase in continuous cultures for more than 500 h. For these expression systems the strong inducible promoter systems GAL7 and methanol oxidase, respectively, were used. The induction of alpha-galactosidase synthesis by galactose in SU50B is limited by the low galactose uptake. Apart from that, at high dilution rates, the glucose repression is substantial, and a maximal expression level of 28.6 mg of extracellular alpha-galactosidase.g (dry weight) of biomass-1 could be obtained. In H. polymorpha, the induction of alpha-galactosidase synthesis, in addition to methanol oxidase synthesis using formaldehyde, is very effective up to 42 mg of extracellular alpha-galactosidase.g (dry weight) of biomass-1. Productivities in terms of specific production rate enable a good comparison with those of other heterologous expression systems in the literature. The productivities found with S. cerevisiae SU50B and H. polymorpha, 3.25 and 5.5 mg of alpha-galactosidase.g of biomass-1.liter-1.h-1, respectively, rank among the highest reported in the literature. Enzyme production and secretion in H. polymorpha are more complex. A two-peaked optimum is found in enzyme production. No clear explanation of this phenomenon can be given.
Antagonistic Effect of Nonpathogenic
Fusarium oxysporum
Fo47 and Pseudobactin 358 upon Pathogenic
Fusarium oxysporum
f. sp.
dianthi
Authors: Lemanceau Philippe , Bakker Peter A. H. M. , De Kogel Willem Jan , Alabouvette Claude , Schippers Bob
Published: January 2020

Pseudobactin production by
Pseudomonas putida
WCS358 significantly improves biological control of fusarium wilt caused by nonpathogenic
Fusarium oxysporum
Fo47b10 (P. Lemanceau, P. A. H. M. Bakker, W. J. de Kogel, C. Alabouvette, and B. Schippers, Appl. Environ. Microbiol. 58:2978-2982, 1992). The antagonistic effect of Fo47b10 and purified pseudobactin 358 was studied by using an in vitro bioassay. This bioassay allows studies on interactions among nonpathogenic
F. oxysporum
Fo47b10, pathogenic
F. oxysporum
f. sp.
dianthi
WCS816, and purified pseudobactin 358, the fluorescent siderophore produced by
P. putida
WCS358. Both nonpathogenic and pathogenic
F. oxysporum
reduced each other's growth when grown together. However, in these coinoculation experiments, pathogenic
F. oxysporum
WCS816 was relatively more inhibited in its growth than nonpathogenic
F. oxysporum
Fo47b10. The antagonism of nonpathogenic
F. oxysporum
against pathogenic
F. oxysporum
strongly depends on the ratio of nonpathogenic to pathogenic
F. oxysporum
densities: the higher this ratio, the stronger the antagonism. This fungal antagonism appears to be mainly associated with the competition for glucose. Pseudobactin 358 reduced the growth of both
F. oxysporum
strains, whereas ferric pseudobactin 358 did not; antagonism by pseudobactin 358 was then related to competition for iron. However, the pathogenic
F. oxysporum
strain was more sensitive to this antagonism than the nonpathogenic strain. Pseudobactin 358 reduced the efficiency of glucose metabolism by the fungi. These results suggest that pseudobactin 358 increases the intensity of the antagonism of nonpathogenic
F. oxysporum
Fo47b10 against pathogenic
F. oxysporum
WCS816 by making WCS816 more sensitive to the glucose competition by Fo47b10.
Detection of hepatitis A virus in sewage sludge by antigen capture polymerase chain reaction
Authors: Graff J , Ticehurst J , Flehmig B
Published: January 2020

Antigen capture polymerase chain reaction (PCR) was tested as a sensitive and rapid method for detecting hepatitis A virus (HAV) in raw sewage sludge. The antigen capture PCR was performed both with and without solid-phase virus-catching monoclonal antibodies. Similar results proved that both methods were equally sensitive. Sewage sludge samples from different regions in Germany were examined for evidence of HAV contamination by antigen capture PCR. This method of detection was compared with that used in a previous study of these sewage sludge samples, in which the HAV was detected through indirect immunofluorescence after cell culture inoculation. The results obtained by antigen capture PCR matched those obtained in the earlier cell culture investigations, when HAV was detected in raw as well as digested sewage sludge samples. The advantage of the PCR method, however, lies in the fact that it needs only two days while the cell culture propagation of HAV takes about 8 to 10 weeks.
Dormancy in Stationary-Phase Cultures of
Micrococcus luteus
: Flow Cytometric Analysis of Starvation and Resuscitation
Authors: Kaprelyants Arseny S. , Kell Douglas B.
Published: January 2020

Cultures of the copiotrophic bacterium
Micrococcus luteus
were stored in spent growth medium for an extended period of time following batch culture. After an initial decrease, the total cell counts remained constant at approximately 60 to 70% of the counts at the beginning of storage. The level of viability, as judged by plate counts, decreased to less than 0.05%, while respiration and the ability to accumulate the lipophilic cation rhodamine 123 decreased to undetectable levels. However, using penicillin pretreatment (to remove viable cells) and flow cytometry and by monitoring both the total and viable counts, we found that at least 50% of the cells in populations of 75-day-old cultures were not dead but were dormant. Resuscitation in liquid medium was accompanied by the appearance of a population of larger cells, which could accumulate rhodamine 123 and reduce the dye 5-cyano-2,3-ditolyl tetrazolium chloride to a fluorescent formazan, while a similar fraction of the population was converted to colony-forming, viable cells. We surmise that dormancy may be far more common than death in starving microbial cultures.
Purification and characterization of a new xylanase (APX-II) from the fungus Aureobasidium pullulans Y-2311-1
Authors: Li X L , Zhang Z Q , Dean J F , Eriksson K E , Ljungdahl L G
Published: January 2020

Aureobasidium pullulans Y-2311-1 produced four major xylanases (EC 3.2.1.8) with pI values of 4.0, 7.3, 7.9, and 9.4 as revealed by isoelectric focusing and zymogram analysis when grown for 4 days on 1.0% oat spelt xylan. The enzyme with a pI of 9.4 was purified by ammonium sulfate precipitation, chromatography on a DEAE-Sephadex A-50 column, and gel filtration with a Sephadex G-75 column. The enzyme had a mass of about 25 kDa as determined by both sodium dodecyl sulfate-polyacrylamide gel electrophoresis and gel filtration chromatography. The purified enzyme had a Km of 7.6 mg . ml(-1) and Vmax of 2,650 micromol . min(-1) . mg(-1) for birchwood xylan at 28 degrees C and pH 4.5. It lacked activity towards carboxymethylcellulose, cellobiose, starch, mannan, p-nitrophenyl (pNP)-beta-D-xylopyranoside, pNP-beta-D-glucopyranoside, pNP-alpha-D-glucopyranoside, pNP-beta-D-cellobioside, pNP-beta-D-fucopyranoside, or pNP-alpha-D-galactopyranoside. The predominant end products of birchwood xylan or xylohexaose hydrolysis were xylobiose and xylose. The enzyme had the highest activity of pH 4.8 and 54 degrees C. Sixty percent of the activity remained after the enzyme had been incubated at 55 degrees C and pH 4.5 for 30 min. The sequence of the first 68 amino acid residues at the amino terminus showed homology to those of several other xylonases. Immunoblot analysis with antiserum raised against the purified xylanase revealed that two immunologically related polypeptides of 25 and 22 kDa were produced in A. pullulans cultures containing oat spelt xylan or xylose as carbon sources but not in cultures containing glycerol or glucose.
Use of a simplified cell blot technique and 16S rRNA-directed probes for identification of common environmental isolates
Authors: Braun-Howland E B , Vescio P A , Nierzwicki-Bauer S A
Published: January 2020

A simple technique in which rRNA-targeted oligodeoxynucleotide probes are used to identify bacteria immobilized on membranes is described. By using colony lifts, bacteria are directly transferred from plates to untreated nitrocellulose membranes. Alternatively, cells resuspended from colonies can be applied to membranes by using a vacuum manifold under high-salt conditions. Blotted cells are baked and hybridized under stringent conditions by using standard protocols. Treatment of blotted cells with sodium dodecyl sulfate, urea, formaldehyde, or protease had no apparent effect on hybridization signals. Hybridization to rRNA from cells that had been stored refrigerated for 6 days was readily detected; however, fivefold more cells (approximately 10(7) cells) were required to obtain hybridization signals comparable to those generated by cells not subjected to storage. The sequences of oligonucleotide probes specific for Pseudomonas cepacia, Comamonas testosteroni, and Acinetobacter calcoaceticus and a group probe identifying Pseudomonas aeruginosa, Pseudomonas mendocina, Pseudomonas fluorescens, Comamonas acidovorans, and "Flavobacterium" lutescens are presented. In conjunction with the colony lift hybridization procedure, bacteria isolated from river water were identified by using these probes.
Isolation and characterization of an N-methylcarbamate insecticide-degrading methylotrophic bacterium
Authors: Topp E , Hanson R S , Ringelberg D B , White D C , Wheatcroft R
Published: January 2020

A gram-negative bacterium which hydrolyzed aryl N-methylcarbamate insecticides was isolated from an agricultural soil which quickly degraded these pesticides. This organism, designated strain ER2, grew on carbofuran as a sole source of carbon and nitrogen with a doubling time of 3 h in a mineral salts medium. The aromatic nucleus of the molecule was not metabolized, and carbofuran 7-phenol accumulated as the end product of metabolism. The insecticides carbaryl, bendiocarb, and propoxur were similarly hydrolyzed, with each yielding the corresponding phenol. Strain ER2 contained two plasmids (120 and 130 kb). A probe cloned from the pDL11 plasmid of Achromobacter sp. strain WM111, which encodes the carbofuran hydrolase (mcd) gene (P. H. Tomasek and J. S. Karns, J. Bacteriol. 171:4038-4044, 1989), hybridized to the 120-kb plasmid. Restriction fragment profiles of pDL11 and strain ER2 plasmid DNAs suggested that the 120-kb plasmid of strain ER2 is very similar to pDL11. On the basis of the results of biochemical tests, 16S rRNA sequence analysis, and membrane lipid analyses, strain ER2 was found to be a phylogenetically unique type II methylotroph. The constitutive carbofuran hydrolase activity in glucose-grown cells increased sevenfold when strain ER2 was grown in the presence of 100 mg of carbofuran per liter as the sole source of carbon and nitrogen or as the sole nitrogen source in the presence of glucose. Growth on carbofuran resulted in the induction of enzymes required for methylamine-dependent respiration and the serine pathway of formaldehyde assimilation. These results indicate that the carbofuran hydrolase mcd gene is conserved on a plasmid found in organisms from different geographic areas and that the specific activity of carbofuran degradation may increase in response to carbofuran treatment.
Variations in the uptake and metabolism of peptides and amino acids by mixed ruminal bacteria in vitro
Authors: Armstead I P , Ling J R
Published: January 2020

Mixed ruminal bacteria, isolated from sheep (Q and W) fed a concentrate and hay diet, were anaerobically incubated with either 14C-peptides or 14C-amino acids. Experiment 1 showed that uptake of both 14C-labeled substrates was rapid, but the rate for amino acids was twofold greater than for peptides (molecular weight, 1,000 to 200) initially but was similar after 10 min. Experiment 2 demonstrated that metabolism was also rapid; at least 90% of either 14C-labeled substrate was metabolized by 3 min. Of the radioactivity remaining in bacteria, approximately 30% was in the form of 14C-amino acids, but only in leucine, tyrosine, and phenylalanine. Supernatant radioactivity was contained only in tyrosine, phenylalanine, and mostly proline for incubations with 14C-amino acids but in up to 10 amino acids when 14C-peptides were the substrates. Short-term incubations (< 5 min; experiment 3) confirmed previous uptake patterns and showed that the experimental system was responsive to substrate competition. Experiment 4 demonstrated that bacteria from sheep Q possessed initial and maximum rates of 14C-amino acid uptake approximately fourfold greater (P < 0.01) than those of 14C-peptides, but with no significant differences (P > 0.1) between four 14C-peptide substrate groups with molecular weights of 2,000 to < 200. By contrast, bacteria from sheep W showed no such distinctions (P > 0.1) between rates for 14C-peptides and 14C-amino acids. Calculations suggested that peptides could supply from 11 to 35% and amino acids could supply from 36 to 68% of the N requirements of mixed ruminal bacteria.(ABSTRACT TRUNCATED AT 250 WORDS)
Direct Electron Microscopy Study on the Morphological Diversity of Bacteriophage Populations in Lake Plußsee
Authors: Demuth Jutta , Neve Horst , Witzel Karl-Paul
Published: January 2020

Direct electron microscopy of bacteriophages adsorbed to a carbon film without prior enrichment by specific host strains or concentration by physical or chemical methods was used to study the morphological diversity of natural bacteriophage assemblages in a North German lake. All samples contained a mixture of morphologically different tailed viruses, which were regarded as bacteriophages. Most of them had isometric heads and long noncontractile tails, belonging to morphotype B1 (
Siphoviridae
). In addition, members of morphotypes A1 (
Myoviridae
), B2 (
Siphoviridae
with elongated heads), and C1 (
Podoviridae
) were present in lower numbers. Only one cubic virus was detected, while no filamentous or pleomorphic phages were found. Up to 11 different phages per sample, and a total of 39 phages when all samples were considered together, could be distinguished by morphological criteria. The total number of phages was estimated to be on the order of 10
8
/ml.
Resistance to Co-Occurring Phages Enables Marine
Synechococcus
Communities To Coexist with Cyanophages Abundant in Seawater
Authors: Waterbury John B. , Valois Frederica W.
Published: January 2020

Recent reports documenting very high viral abundances in seawater have led to increased interest in the role of viruses in aquatic environments and a resurgence of the hypothesis that viruses are significant agents of bacterial mortality.
Synechococcus
spp., small unicellular cyanobacteria that are important primary producers at the base of the marine food web, were used to assess this hypothesis. We isolated a diverse group of
Synechococcus
phages that at times reach titers of between 10
3
and 10
4
cyanophages per ml in both inshore and offshore waters. However, despite their diversity and abundance, we present evidence in support of the hypothesis that lytic phages have a negligible effect in regulating the densities of marine
Synechococcus
populations. Our results indicate that these bacterial communities are dominated by cells resistant to their co-occurring phages and that these viruses are maintained by scavenging on the relatively rare sensitive cells in these communities.
Near-Bottom Pelagic Bacteria at a Deep-Water Sewage Sludge Disposal Site
Authors: Takizawa M. , Straube W. L. , Hill R. T. , Colwell R. R.
Published: January 2020

The epibenthic bacterial community at deep-ocean sewage sludge disposal site DWD-106, located approximately 106 miles (ca. 196 km) off the coast of New Jersey, was assessed for changes associated with the introduction of large amounts of sewage sludge. Mixed cultures and bacterial isolates obtained from water overlying sediment core samples collected at the deep-water (2,500 m) municipal sewage disposal site were tested for the ability to grow under in situ conditions of temperature and pressure. The responses of cultures collected at a DWD-106 station heavily impacted by sewage sludge were compared with those of samples collected from a station at the same depth which was not contaminated by sewage sludge. Significant differences were observed in the ability of mixed bacterial cultures and isolates from the two sites to grow under deep-sea pressure and temperature conditions. The levels of sludge contamination were established by enumerating
Clostridium perfringens
, a sewage indicator bacterium, in sediment samples from the two sites. The results of hybridization experiments in which DNAs extracted directly from the water overlying sediment core samples were used indicate that the reference site epibenthic community, the disposal site epibenthic community, and the community in a surface sludge plume share many members. Decreased culturability of reference site mixed cultures in the presence of sewage sludge was observed. Thus, the culturable portions of both the autochthonous and allochthonous bacterial communities at the disposal site may be inhibited in situ, the former by sewage sludge and the latter by high pressure and low temperature.
Metabolism of chlorinated guaiacols by a guaiacol-degrading Acinetobacter junii strain
Authors: González B , Acevedo C , Brezny R , Joyce T
Published: January 2020

The metabolism of chlorinated guaiacols by a pure bacterial strain identified by its ability to use guaiacol as the sole carbon and energy source was studied. This strain, identified as Acinetobacter junii 5ga, was unable to grow on several chlorinated guaiacols and catechols. However, strain 5ga grown on guaiacol degraded 4- and 5-chloroguaiacol and 4,5-dichloroguaiacol. Under the same conditions, these cells did not degrade 6-chloroguaiacol, 4,6-dichloroguaiacol, 4,5,6-trichloroguaiacol, or tetrachloroguaiacol, suggesting that the substitution at the 6 position in the ring prevents metabolism of the compound. Degradation of 4-chloroguaiacol was dependent on the initial ratio between the chlorinated compound and viable cells. Transient formation of chlorocatechols resulting from incubation of cells with 4-chloroguaiacol or 4,5-dichloroguaiacol was suggested by UV spectroscopy. Gas chromatography analyses of samples from cultures of strain 5ga grown on guaiacol and incubated with 4- and 4,5-dichloroguaiacol confirmed the presence of 4-chlorocatechol and 4,5-dichlorocatechol, respectively. The formation of the latter was corroborated by gas chromatography-mass spectrometry. Thus, this strain is able to initiate metabolism of specific chlorinated guaiacols by O-demethylation. The starting chlorinated guaiacols and their O-demethylated metabolites inhibited the growth of A. junii 5ga on guaiacol.
The specific growth rate of Pseudomonas putida PAW1 influences the conjugal transfer rate of the TOL plasmid
Authors: Smets B F , Rittmann B E , Stahl D A
Published: January 2020

The kinetics of the conjugal transfer of a TOL plasmid were investigated by using Pseudomonas putida PAW1 as the donor strain and P. aeruginosa PAO 1162 as the recipient strain. Short-term batch mating experiments were performed in a nonselective medium, while the evolution of the different cell types was determined by selective plating techniques. The experimental data were analyzed by using a mass action model that describes plasmid transfer kinetics. This method allowed analysis of the mating experiments by a single intrinsic kinetic parameter for conjugal plasmid transfer. Further results indicated that the specific growth rate of the donor strain antecedent to the mating experiment had a strong impact on the measured intrinsic plasmid transfer rate coefficient, which ranged from 1 x 10(-14) to 5 x 10(-13) ml per cell per min. Preliminary analysis suggested that the transfer rates of the TOL plasmid are large enough to maintain the TOL plasmid in a dense microbial community without selective pressures.
Effects of Motility and Adsorption Rate Coefficient on Transport of Bacteria through Saturated Porous Media
Authors: Camper Anne K. , Hayes Jason T. , Sturman Paul J. , Jones Warren L. , Cunningham Alfred B.
Published: January 2020

Three strains of
Pseudomonas fluorescens
with different motility rates and adsorption rate coefficients were injected into porous-medium reactors packed with l-mm-diameter glass spheres. Cell breakthrough, time to peak concentration, tailing, and cell recovery were measured at three interstitial pore velocities (higher than, lower than, and much lower than the maximal bacterial motility rate). All experiments were done with distilled water to reduce the effects of growth and chemotaxis. Contrary to expectations, motility did not result in either early breakthrough or early time to peak concentration at flow velocities below the motility rate. Bacterial size exclusion effects were shown to affect breakthrough curve shape at the very low flow velocity, but no such effect was seen at the higher flow velocity. The tendency of bacteria to adsorb to porous-medium surfaces, as measured by adsorption rate coefficients, profoundly influenced transport characteristics. Cell recoveries were shown to be correlated with the ratio of advective to adsorptive transport in the reactors. Adsorption rate coefficients were found to be better predictors of microbial transport phenomena than individual characteristics, such as size, motility, or porous-medium hydrodynamics.
Enumeration of Vibrio vulnificus on membrane filters with a fluorescently labeled oligonucleotide probe specific for kingdom-level 16S rRNA sequences
Authors: Heidelberg J F , O'Neill K R , Jacobs D , Colwell R R
Published: January 2020

Vibrio vulnificus was enumerated on membrane filters after hybridization with a fluorescent oligonucleotide eubacterial probe. Cells were hybridized in liquid buffer or directly on membrane filters. There was no significant difference between fluorescent oligonucleotide direct counts and acridine orange direct counts (P > 0.05). Liquid buffer hybridization was preferable to direct filter hybridization.
Effects of glucose, growth temperature, and pH on listeriolysin O production in Listeria monocytogenes
Authors: Datta A R , Kothary M H
Published: January 2020

Expression of listeriolysin O of Listeria monocytogenes as a function of different growth conditions was studied by performing a direct hemolysin assay, immunoblotting experiments, and an enzyme-linked immunosorbent assay. Expression of listeriolysin O was reduced at a lower growth temperatures (26 degrees C) and at higher glucose concentrations (> or = 0.3%) in the growth media. The effect of glucose appeared to be due to a change in the pH of the growth media.
Chromate Reduction by Resting Cells of
Agrobacterium radiobacter
EPS-916
Authors: Llovera Santiago , Bonet Ramon , Simon-Pujol Maria D. , Congregado Francisco
Published: January 2020

Resting cells of
Agrobacterium radiobacter
EPS-916 grown on glucose, fructose, maltose, lactose, mannitol, or glycerol reduced 0.5 mM chromate. However, resting cells of strain EPS-916 grown on glutamate or succinate did not reduce chromate. The ability of washed cells to reduce chromate was correlated with their redox potential.
A comparison of NO and N2O production by the autotrophic nitrifier Nitrosomonas europaea and the heterotrophic nitrifier Alcaligenes faecalis
Authors: Anderson I C , Poth M , Homstead J , Burdige D
Published: January 2020

Soil microorganisms are important sources of the nitrogen trace gases NO and N2O for the atmosphere. Present evidence suggests that autotrophic nitrifiers such as Nitrosomonas europaea are the primary producers of NO and N2O in aerobic soils, whereas denitrifiers such as Pseudomonas spp. or Alcaligenes spp. are responsible for most of the NO and N2O emissions from anaerobic soils. It has been shown that Alcaligenes faecalis, a bacterium common in both soil and water, is capable of concomitant heterotrophic nitrification and denitrification. This study was undertaken to determine whether heterotrophic nitrification might be as important a source of NO and N2O as autotrophic nitrification. We compared the responses of N. europaea and A. faecalis to changes in partial O2 pressure (pO2) and to the presence of typical nitrification inhibitors. Maximal production of NO and N2O occurred at low pO2 values in cultures of both N. europaea (pO2, 0.3 kPa) and A. faecalis (pO2, 2 to 4 kPa). With N. europaea most of the NH4+ oxidized was converted to NO2-, with NO and N2O accounting for 2.6 and 1% of the end product, respectively. With A. faecalis maximal production of NO occurred at a pO2 of 2 kPa, and maximal production of N2O occurred at a pO2 of 4 kPa. At these low pO2 values there was net nitrite consumption. Aerobically, A. faecalis produced approximately the same amount of NO but 10-fold more N2O per cell than N. europaea did. Typical nitrification inhibitors were far less effective for reducing emissions of NO and N2O by A. faecalis than for reducing emissions of NO and N2O by N. europaea.(ABSTRACT TRUNCATED AT 250 WORDS)
New medium for the simultaneous detection of total coliforms and Escherichia coli in water
Authors: Brenner K P , Rankin C C , Roybal Y R , Stelma G N , Scarpino P V , Dufour A P
Published: January 2020

A new membrane filter agar medium (MI agar) containing a chromogen, indoxyl-beta-D-glucuronide, and a fluorogen, 4-methylumbelliferyl-beta-D-galactopyranoside, was developed to simultaneously detect and enumerate Escherichia coli and total coliforms (TC) in water samples on the basis of their enzyme activities. TC produced beta-galactosidase, which cleaved 4-methylumbelliferyl-beta-D-galactopyranoside to form 4-methylumbelliferone, a compound that fluoresced under longwave UV light (366 nm), while E. coli produced beta-glucuronidase, which cleaved indoxyl-beta-D-glucuronide to form a blue color. The new medium TC and E. coli recoveries were compared with those of mEndo agar and two E. coli media, mTEC agar and nutrient agar supplemented with 4-methylumbelliferyl-beta-D-glucuronide, using natural water samples and spiked drinking water samples. On average, the new medium recovered 1.8 times as many TC as mEndo agar, with greatly reduced background counts (< or = 7%). These differences were statistically significant (significance level, 0.05). Although the overall analysis revealed no statistically significant difference between the E. coli recoveries on MI agar and mTEC agar, the new medium recovered more E. coli in 16 of 23 samples (69.6%). Both MI agar and mTEC agar recovered significantly more E. coli than nutrient agar supplemented with 4-methylumbelliferyl-beta-D-glucuronide. Specificities for E. coli, TC, and noncoliforms on MI agar were 95.7% (66 of 69 samples), 93.1% (161 of 173 samples), and 93.8% (61 of 65 samples), respectively. The E. coli false-positive and false-negative rates were both 4.3%. This selective and specific medium, which employs familiar membrane filter technology [corrected] to analyze several types of water samples, is less expensive than the liquid chromogen and fluorogen media and may be useful for compliance monitoring of drinking water.
Pulmonary clearance and inflammatory response in C3H/HeJ mice after intranasal exposure to Pseudomonas spp
Authors: George S E , Kohan M J , Gilmour M I , Taylor M S , Brooks H G , Creason J P , Claxton L D
Published: January 2020

The environmental release of engineered microorganisms has caused health and environmental concerns. In this study, an animal model was used to examine health effects following pulmonary exposure to environmental and clinical isolates. In order to rule out the possibility that an adverse response was caused by endotoxin, 50% lethal doses (LD50) were determined, when possible, with endotoxin-sensitive (C3HeB/FeJ) and endotoxin-resistant (C3H/HeJ) mice by using both environmental isolates (Pseudomonas aeruginosa BC16, BC17, BC18, and AC869 and Pseudomonas maltophilia BC6) and clinical isolates (P. aeruginosa PAO1 and DG1). The LD50 of strains AC869, DG1, and PAO1 are 1.05 x 10(7), 6.56 x 10(6), and 1.02 x 10(7) CFU, respectively, in C3HeB/FeJ mice and 1.05 x 10(7), 1.00 x 10(7), and 2.75 x 10(6) CFU, respectively, in C3H/HeJ mice. Strains BC17 and BC18 were not lethal to the animals. On the basis of the LD50 data, an appropriate sublethal dose (approximately 10(6) CFU) was selected. Animals were challenged intranasally with microorganisms, and clearance from the lungs and nasal cavity was determined. Strains BC17, BC18, and AC869 were not detected in lungs or nasal washes 14 days following treatment. Strains BC6, BC16, and DG1 were recovered from the nasal cavities at the end of the experiment. Only strain PAO1 was detected in lungs and in nasal cavities 14 days after treatment. At selected intervals following treatment, the percentages of polymorphonuclear leukocytes and lymphocytes in bronchoalveolar lavage samples were determined. P. aeruginosa AC869, PAO1, and DG1 elicited a relatively strong inflammatory response which was indirectly related to lung clearance.(ABSTRACT TRUNCATED AT 250 WORDS)
Microbial Decomposition of Elm and Oak Leaves in a Karst Aquifer
Authors: Eichem Angela C. , Dodds Walter K. , Tate Cathy M. , Edler Chris
Published: January 2020

Dry Chinquapin oak (
Quercus macrocarpa
) and American elm (
Ulmus americana
) leaves were placed in four microcosms fed by groundwater springs to monitor changes in dry mass, ash-free dry mass, and microbial activity over a 35-day period. Oxygen microelectrodes were used to measure microbial activity and to estimate millimeter-scale heterogeneity in that activity. Oak leaves lost mass more slowly than elm leaves. Generally, there was a decrease in total dry weight over the first 14 days, after which total dry weight began to increase. However, there were consistent decreases in ash-free dry mass over the entire incubation period, suggesting that the material remaining after initial leaf decomposition trapped inorganic particles. Microbial activity was higher on elm leaves than on oak leaves, with peak activity occurring at 6 and 27 days, respectively. The level of oxygen saturation on the bottom surface of an elm leaf ranged between 0 and 75% within a 30-mm
2
area. This spatial heterogeneity in O
2
saturation disappeared when the water velocity increased from 0 to 6 cm s
-1
. Our results suggest that as leaves enter the groundwater, they decompose and provide substrate for microorganisms. The rate of decomposition depends on leaf type, small-scale variations in microbial activity, water velocity, and the length of submersion time. During the initial stages of decomposition, anoxic microzones are formed that could potentially be important to the biogeochemistry of the otherwise oxic aquifer.
Variation in Nitrogen Utilization in
Acremonium coenophialum
Isolates
Authors: Ferguson N. H. , Rice J. S. , Allgood N. G.
Published: January 2020

Acremonium coenophialum
, a fungal endosymbiont in tall fescue, is responsible for the production of alkaloid toxins. Animals grazing endophyte-infected tall fescue often show toxicosis. In marginal environments, the endophyte is important for long-term survival of tall fescue. Few differences in endophyte isolates from individual tall fescue plants have been reported. To aid development of a toxicosis-free tall fescue, it is important to identify differences in endophyte isolates. This report describes variation in nitrogen utilization in a defined culture medium by endophyte isolates from Kentucky-31 tall fescue. Overall, the best nitrogen sources for dry weight production of mycelium were proline and potassium nitrate. Thirty-four isolates grown on agar-solidified defined media with single nitrogen sources showed variation in nitrogen utilization. Fifty percent of the isolates were unable to utilize two or more amino acids. Manipulation of endophyte variation could lead to development of a toxicosis-free tall fescue cultivar.
Cloning and expression of the transposable chlorobenzoate-3,4-dioxygenase genes of Alcaligenes sp. strain BR60
Authors: Nakatsu C H , Wyndham R C
Published: January 2020

Growth on 3-chlorobenzoate was found to induce the enzymes of the protocatechuate meta ring fission pathway in Alcaligenes sp. strain BR60. The chlorobenzoate catabolic genes, designated cba, were localized to a 3.7-kb NotI-EcoRI fragment within the nonrepeated region of the composite transposon Tn5271. The cba genes were cloned onto two broad-host-range vectors and expressed in Escherichia coli and Alcaligenes sp. strain BR6024. In E. coli, expression of the cba genes with the IPTG (isopropyl-beta-D-thiogalactopyranoside)-inducible tac promoter of the IncQ vector pMMB66HE resulted in the production of protocatechuate and chlorodihydroxybenzoate metabolites of 3-chlorobenzoate. Expression of this construct in one orientation resulted in the formation of two polypeptides 51 and 42 kDa in size. This result was confirmed by subcloning into pGEM3Zf and then incorporating L-35S-methionine into newly synthesized proteins, using the thermally regulated T7 polymerase-promoter system. Introduction of the NotI-EcoRI fragment into Alcaligenes sp. strain BR6024 (Cba-P), using the IncP broad-host-range, mobilizable plasmid pBW13, restored the 3-chlorobenzoate-degradative phenotype and resulted in the accumulation of protocatechuate and chlorodihydroxybenzoate intermediates. The data indicate that a two-component dioxygenase specified by Tn5271 oxidizes 3-chlorobenzoate at the 3,4- or 4,5-positions. This activity extends the range of pathways for chloroaromatic compounds known to be functional in the environment. The new pathway avoids the toxicity attributed to the accumulation of chlorocatechol metabolites in bacteria degrading chlorobenzoates.
Anaerobic Nitrate Respiration by
Erwinia carotovora
subsp.
atroseptica
during Potato Tuber Invasion
Authors: Smid Eddy J. , Jansen Antonius H. J. , Tuijn Cees J.
Published: January 2020

The in planta induction of anaerobic nitrate respiration by
Erwinia carotovora
subsp.
atroseptica
in relation to the in situ oxygen status in soft rotting potato tubers has been investigated. In vitro experiments have shown that nitrate was required for the induction of respiratory nitrate reductase activity in
E. carotovora.
In addition, oxygen was found to repress this activity. Expression of respiratory nitrate reductase was found in
E. carotovora
cells extracted from soft rotting potato tuber tissue. However, the rate of nitrite production in these cells was approximately 70-fold lower than the rate recorded in fully induced anaerobic cultures. Oxygen measurements in soft rotting potato tubers indicated that the invading bacteria encounter the lowest oxygen concentration at the interphase between healthy and macerated tissue. Consequently, growth of bacteria present in this specific zone will be stimulated by nitrate which is present in sufficient amounts in tuber tissue. A high nitrate content of the tuber will most likely facilitate the proliferation of
E. carotovora
in the tuber tissue.
Purification and characterization of two 1,4-beta-xylan endohydrolases from the rumen fungus Neocallimastix frontalis
Authors: Gomez de Segura B , Fevre M
Published: January 2020

Two beta-endoxylanases produced by Neocallimastix frontalis have been purified by ammonium sulfate precipitation, gel filtration, and ion-exchange chromatography. Xylanase I is a nonglycosylated protein with an apparent molecular mass of 45 kDa. Xylanase II is a glycoprotein with an apparent molecular mass of 70 kDa. The pH optima of these enzymes were 5.5 and 6, respectively, and the temperature optimum was 55 degrees C for each enzyme. The endo mode of action of the enzymes was revealed by thin-layer chromatography of xylan hydrolysates. Antibodies raised against each purified protein exhibited no cross-reaction, confirming the biochemical specificities of the enzymes. Both enzymes exhibited carboxymethyl cellulase activity, and xylanase I was absorbed on crystalline cellulose, indicating that these enzymes might belong to the F family of beta-1,4-glycanases.
Isotactic polypropylene biodegradation by a microbial community: physicochemical characterization of metabolites produced
Authors: Cacciari I , Quatrini P , Zirletta G , Mincione E , Vinciguerra V , Lupattelli P , Giovannozzi Sermanni G
Published: January 2020

From a selective enrichment culture prepared with different soil samples on starch-containing polyethylene we isolated four microaerophilic microbial communities able to grow on this kind of plastic with no additional carbon source. One consortium, designated community 3S, was tested with pure isotactic polypropylene to determine whether the consortium was able to degrade this polymer. Polypropylene strips were incubated for 5 months in a mineral medium containing sodium lactate and glucose in screw-cap bottles. Dichloromethane crude extracts of the cultures revealed that the weight of extracted materials increased with incubation time, while the polypropylene sample weight decreased. The extracted materials were characterized by performing chromatographic and spectral analyses (thin-layer chromatography, liquid chromatography, gas chromatography-mass spectrometry, infrared spectrometry, nuclear magnetic resonance). Three main fractions were detected and analyzed; a mixture of hydrocarbons at different degrees of functionalization was found together with a mixture of aromatic esters, as the plasticizers usually added to polyolefinic structures.