bluuebunny/crossref_metadata_2025 huggingface dataset:
Examination of Lipopolysaccharide (O-Antigen) Populations of
Thiobacillus ferrooxidans
from Two Mine Tailings
Authors: Southam G. , Beveridge T. J.
Published: January 2020

Net acid-generating capacities of 39.74 kg of H
2
SO
4
per ton (ca. 0.05 kg/kg) (pH 2.68) for the Lemoine copper mine tailings (closed ca. 8 years ago; located 40 km west of Chibougamau, Quebec, Canada) and 16.07 kg of H
2
SO
4
per ton (ca. 0.02 kg/kg) (pH 3.01) for the Copper Rand tailings (in current use and 50 km distant [east] from those of Lemoine) demonstrate that these sulfide tailings can support populations of acidophilic thiobacilli. Oxidized regions in both tailings environments were readily visible, were extremely acidic (Lemoine, pH 2.36; Copper Rand, pH 3.07), and provided natural isolates for our study. A 10% (wt/vol) oxalic acid treatment, which solubilizes both ferric sulfate and ferric hydroxide precipitates (B. Ramsay, J. Ramsay, M. deTremblay, and C. Chavarie, Geomicrobiol. J. 6:171-177, 1988), enabled the recovery of intact bacterial cells from the tailings material and from liquid synthetic medium for lipopolysaccharide analysis. No viable cells could be cultured after this oxalic acid treatment. Sodium dodecyl sulfate-polyacrylamide gel electro-phoretic profiles of lipopolysaccharides extracted from the Lemoine tailings were complex, indicating a heterogeneous population of
Thiobacillus ferrooxidans.
Six
T. ferrooxidans
subspecies as identified by lipopolysaccharide analysis (i.e., lipopolysaccharide chemotypes) were eventually isolated from a total of 112 cultures from the Lemoine tailings. Using the same isolate and lipopolysaccharide typing techniques, we identified only a single lipopolysaccharide chemotype from 20 cultures of
T. ferrooxidans
isolated from the Copper Rand tailings. This homogeneity of lipopolysaccharide chemotype was much different from what was found for the older Lemoine tailings and may reflect a progressive lipopolysaccharide heterogeneity of
Thiobacillus
isolates as tailings leach and age.
Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans
Authors: Fuhrman J A , McCallum K , Davis A A
Published: January 2020

The extent of the diversity of marine prokaryotes is not well known, primarily because of poor cultivability. However, new techniques permit the characterization of such organisms without culturing, via 16S rRNA sequences obtained directly from biomass. We performed such an analysis by polymerase chain reaction amplification with universal primers on five oligotrophic open-ocean samples: from 100-m (three samples) and 500-m depths in the western California Current (Pacific Ocean) and from a 10-m depth in the Atlantic Ocean near Bermuda. Of 61 clones, 90% were in clusters of two or more related marine clones obtained by ourselves or others. We report 15 clones related to clone SAR 11 found earlier near Bermuda (S. J. Giovannoni, T. B. Britschgi, C. L. Moyer, and K. G. Field, Nature [London] 345:60-63, 1990), 11 related to marine cyanobacteria, 9 clustered in a group affiliated with gram-positive bacteria, 9 in an archaeal cluster we recently described (mostly from the 500-m sample), 4 in a novel gamma-proteobacterial cluster, and 6 in three two-membered clusters (including other archaea). One clone was related to flavobacteria. Only the cyanobacteria plus one other clone, related to Roseobacter denitrificans (formerly Erythrobacter longus Och114), were within 10% sequence identity to any previously sequenced cultured organism in a major data base. We never found more than two occurrences of the same sequence in a sample, although four times we found identical sequences between samples, two of which were between oceans; one of these sequences was also identical to SAR 11.(ABSTRACT TRUNCATED AT 250 WORDS)
Rapid detection of salmonellae in poultry with the magnetic immuno-polymerase chain reaction assay
Authors: Fluit A C , Widjojoatmodjo M N , Box A T , Torensma R , Verhoef J
Published: January 2020

Rapid detection of salmonellae in chicken meat was accomplished by using the magnetic immuno-polymerase chain reaction assay (MIPA). A direct polymerase chain reaction assay performed with chicken meat spiked with Salmonella typhimurium resulted in poor sensitivity (approximately 10(7) CFU/g of meat). The use of immunoseparation with a Salmonella serogroup B-specific monoclonal antibody improved the sensitivity, but enrichment was required for the detection of low levels of contamination. Enrichment for 6 h in either buffered peptone water, lactose broth containing tergitol-7, or selenite-cystine broth resulted in the detection of an initial inoculum of 100 CFU per g of meat. Enrichment of the salmonellae present on 25 g of spiked chicken meat for 24 h in either buffered peptone water or selenite-cystine broth before detection by the MIPA yielded a detection limit of approximately 0.1 CFU/g of meat. A detection limit of approximately 1 CFU/g of meat was obtained when the spiked meat was stored at -20 degrees C before enrichment for 24 h and analysis with the MIPA. Although the MIPA was developed for S. typhimurium, a MIPA in which a panel of six monoclonal antibodies specific for Salmonella serogroups A through E was used detected the presence of 0.1 CFU of Salmonella enteritidis per g of chicken meat. These data indicate that the method is applicable to other commonly isolated serotypes.
Growth, Nitrogen Fixation, and Spectral Attenuation in Cultivated
Trichodesmium
Species
Authors: Prufert-Bebout Lee , Paerl Hans W. , Lassen Carsten
Published: January 2020

Physiological studies of
Trichodesmium
species have been hindered by difficulties in maintaining actively growing, nitrogen-fixing cultures. Previous cultivation successes have not been widely duplicated. We present here a simple modified seawater medium and handling techniques which have been used to maintain actively growing
Trichodesmium thiebautii
in laboratory culture for over 1 year. The cultured population, isolated from coastal Atlantic waters, has a growth rate of 0.23 division day
-1
and exhibits light-dependent nitrogen fixation during exponential growth. Various morphologies, including solitary trichomes, and aggregates (spherical puffs and fusiform tufts) are present during growth. Spectral and scalar irradiance were measured within naturally occurring (coastal Atlantic) aggregates with small (diameter, 50 to 70 μm) spherical fiber-optic sensors. In contrast to naturally occurring puffs, cultivated
Trichodesmium
aggregates exhibited spectral properties consistent with low-light adaptation. Cultivated puff-type aggregates were also examined by using oxygen microelectrodes. The simple medium and approach used for cultivation should be easily reproducible and amenable to further manipulations and modifications useful for physiological studies of
Trichodesmium
spp. in culture.
Purification and Characterization of Alkaline Xylanases from
Bacillus polymyxa
Authors: Morales P. , Madarro A. , Pérez-González J. A. , Sendra J. M. , Piñaga F. , Flors A.
Published: January 2020

By applying different classical and fast protein liquid chromatographic techniques, three xylanases (β-1,4-
d
-xylan xylanhydrolase) were purified to homogeneity from the extracellular enzymatic complex of
Bacillus polymyxa
. The three enzymes (X
34
C, X
34
E, and X
22
) were small proteins of 34, 34, and 22 kDa and basic pIs 9.3, >9.3, and 9.0, respectively. X
34
C and X
34
E are closely related and seem to be isoforms of the same enzyme. However, they differ in some characteristics. The three enzymes had different pH and temperature optima. One of them, X
34
E, showed a high thermal stability. The
V
max
values determined for X
34
C, X
34
E, and X
22
enzymes on oat spelts xylan were 14.9, 85.5, and 64.0 U mg
-1
, respectively, and 16.1, 62.0, and 150.6 U mg
-1
on birchwood xylan. When oat spelts xylan was the substrate used,

K
m

values of 3.4, 2.4, and 1.9 mg ml
-1
were obtained for X
34
C, X
34
E, and X
22
enzymes, respectively, and 0.65, 6.3, and 0.32 mg ml
-1
were the respective

K
m

values determined with birchwood xylan as the substrate. The enzymes were nondebranching endo-β-xylanases. Xylose was one of the products of xylan hydrolysis by xylanases X
34
C and X
34
E, but this monosaccharide was not released by X
22
enzyme. However, neither of the enzymes was able to degrade xylobiose.
Identification of procaryotic repetitive DNA suitable for use as fingerprinting probes
Authors: Waterhouse R N , Glover L A
Published: January 2020

We have developed a method which enables the cloning and identification of procaryotic repetitive DNA suitable for use as DNA fingerprinting probes. The method involves shotgun cloning of restricted genomic DNA with subsequent selection of clones containing repetitive DNA by reverse-probed genomic hybridizations, in which the plasmid DNA clones are probed with labelled genomic DNA. Confirmation that the clones contained repeated sequences was by Southern hybridization, gene copy equivalence, and DNA sequencing. The sequences were used for highly specific and sensitive detection of bacteria and as target sequences for the mediation of chromosomal integration of reporter gene constructs.
Purification and characterization of the extracellular alpha-amylase from Streptococcus bovis JB1
Authors: Freer S N
Published: January 2020

The extracellular alpha-amylase (1,4-alpha-D-glucanglucanohydrolase; EC 3.2.1.1) from maltose-grown Streptococcus bovis JB1 was purified to apparent homogeneity by ion-exchange chromatography (Mono Q). The enzyme had an isoelectric point of 4.50 and an apparent molecular mass of 77,000 Da, as estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The enzyme was rich in acidic and hydrophobic amino acids. The 15-amino-acid NH2-terminal sequence was 40% homologous with the Bacillus subtilis saccharifying alpha-amylase and 27% homologous with the Clostridium acetobutylicum alpha-amylase. alpha-Amylase activity on soluble starch was optimal at pH 5.0 to 6.0. The enzyme was relatively stable between pH 5.5 and 8.5 and at temperatures below 50 degrees C. When soluble potato starch was used as the substrate, the enzyme had a Km of 0.88 mg.ml-1 and a kcat of 2,510 mumol of reducing sugar.min-1.mg of protein-1. The enzyme exhibited neither pullulanase nor dextranase activity and was 40 to 70% as active on amylopectin as on amylose. The major end products of amylose hydrolysis were maltose, maltotriose, and maltotetraose.
Survival of human immunodeficiency virus (HIV), HIV-infected lymphocytes, and poliovirus in water
Authors: Moore B E
Published: January 2020

The potential for human immunodeficiency virus (HIV) to enter domestic sewers via contaminated body fluids such as blood has spurred interest in the survival of this virus in water and wastewater. This study focused on establishing the inactivation of HIV and productively infected lymphocytes in dechlorinated tap water. In addition, HIV survival was compared with that of poliovirus. Results indicated that either free HIV or cell-associated HIV was rapidly inactivated, with a 90% loss of infectivity within 1 to 2 h at 25 degrees C and a 99.9% loss by 8 h. In comparison, poliovirus showed no loss of infectivity over 24 h. The presence of human serum in tap water slowed the rate of HIV inactivation through 8 h but did not stabilize the virus through 24 h. In addition, blood from stage IV AIDS patients was introduced into tap water, and the recovery of HIV was monitored by using both an infectivity assay and polymerase chain reaction amplification of viral sequences. Virally infected cells were no longer detectable after 5 min in dechlorinated tap water, while little diminution in amplifiable sequences was observed over 2 h. Thus, detection of viral sequences by polymerase chain reaction technology should not be equated with risk of exposure to infectious HIV.
Repair and enterotoxin synthesis by Staphylococcus aureus after thermal shock
Authors: Hernández F J , Goyache J , Orden J A , Blanco J L , Doménech A , Suárez G , Gómez-Lucía E
Published: January 2020

To study repair and enterotoxin synthesis, four staphylococcal strains (FRI-100, FRI-137, FRI-472, and S6) were subjected to sublethal heat treatment, transferred to four liquid repair media (1% powdered skim milk in distilled water, complex medium, M9 minimal salt medium, and saline solution), and then incubated at different temperatures. Powdered skim milk proved to be the most efficient medium for promoting the repair of injured cells, particularly at 37 degrees C. Minimal salt medium also gave good results. Salt tolerance also increased at 4 degrees C, although it did not reach normal values. After 6 h of incubation at 37 degrees C in powdered skim milk, strain FRI-100 synthesized detectable amounts of enterotoxin A. After 10 h of incubation in the same medium at the same temperature, enterotoxins were detected in all of the strains.
Degradation of a Sodium Acrylate Oligomer by an
Arthrobacter
sp
Authors: Hayashi Takaya , Mukouyama Masaharu , Sakano Kouichi , Tani Yoshiki
Published: January 2020

Arthrobacter
sp. strain NO-18 was first isolated from soil as a bacterium which could degrade the sodium acrylate oligomer and utilize it as the sole source of carbon. When 0.2% (wt/wt) oligomer was added to the culture medium, the acrylate oligomer was found to be degraded by 70 to 80% in 2 weeks, using gel permeation chromatography. To determine the maximum molecular weight for biodegradation, the degradation test was done with the hexamer, heptamer, and octamer, which were separated from the oligomer mixture by fractional gel permeation chromatography. The hexamer and heptamer were consumed to the extents of 58 and 36%, respectively, in 2 weeks, but the octamer was not degraded. Oligomers with three different terminal groups were synthesized to examine the effect of the different terminal groups on biodegradation, but few differences were found.
Arthrobacter
sp. NO-18 assimilated acrylic acid, propionic acid, glutaric acid, 2-methylglutaric acid, and 1,3,5-pentanetricarboxylic acid. Degradation of the acrylic unit structure by this strain is discussed.
Fate of Enterobacter cloacae JP120 and Alcaligenes eutrophus AEO106(pRO101) in soil during water stress: effects on culturability and viability
Authors: Pedersen J C , Jacobsen C S
Published: January 2020

A sandy loam soil near field capacity moisture content (psi = -0.050 MPa) or air dried (psi = -300 MPa) was inoculated with about 3 x 10(7) CFU of Enterobacter cloacae JP120 and Alcaligenes eutrophus AEO106(pRO101) per g and incubated in 40-g portions at 17 degrees C in closed or open Erlenmeyer flasks. In the field-moist soil, selective plating, direct viable counts, and DNA hybridization showed only minor changes in the numbers of E. cloacae and A. eutrophus cells with time (14 days), and the results obtained with the three detection methods generally agreed. In the air-dried soil, the majority of both bacteria were found as intact DNA-carrying cells that were neither culturable nor viable by the methods employed in this study. The numbers of culturable E. cloacae and A. eutrophus cells dropped to 10(5) and 10(2) CFU/g, respectively, 2 h after inoculation. Direct viable counts showed that only about 1% of the cells detected by immunofluorescence microscopy were viable, but a fraction of viable nonculturable cells of both bacteria was present. A. eutrophus did not tolerate desiccation as well as E. cloacae. Only a minor fraction of the two test organisms regained their culturability or viability after rewetting of the air-dried soil; the number of total heterotrophic culturable bacteria, however, increased more than 10-fold and reached 73% of the level found in the field-moist soil at day 14.
Production and characterization of monoclonal antibodies specific for Shewanella colwelliana exopolysaccharide
Authors: Sledjeski D D , Weiner R M
Published: January 2020

Six monoclonal antibodies were produced to whole cells of Shewanella colwelliana (Aco1 to Aco6) and two (Aco22 to Aco23) to purified exopolysaccharide (EPS). Aco1, -4 to -6, -22, and -23 bound to both the cell surface and the purified EPS, while Aco2 and -3 bound to cells only. The EPS of S. colwelliana was antigenically unique from those of nine other species of marine bacteria that were tested. Mapping studies revealed that all of the EPS-specific monoclonal antibodies bound to the same epitope. This EPS epitope was sensitive to cleavage of ester bonds, but neither pyruvate, acetate, nor terminal nonreducing sugars were required for antigenicity. When S. colwelliana was grown on rich media, most of its EPS was loosely associated with the cell surface.
Chemical disinfection to interrupt transfer of rhinovirus type 14 from environmental surfaces to hands
Authors: Sattar S A , Jacobsen H , Springthorpe V S , Cusack T M , Rubino J R
Published: January 2020

Rhinoviruses can survive on environmental surfaces for several hours under ambient conditions. Hands can readily become contaminated after contact with such surfaces, and self-inoculation may lead to infection. Whereas hand washing is crucial in preventing the spread of rhinovirus colds, proper disinfection of environmental surfaces may further reduce rhinovirus transmission. In this study, the capacities of Lysol Disinfectant Spray (0.1% o-phenylphenol and 79% ethanol), a domestic bleach (6% sodium hypochlorite diluted to give 800 ppm of free chlorine), a quaternary ammonium-based product (7.05% quaternary ammonium diluted 1:128 in tap water), and a phenol-based product (14.7% phenol diluted 1:256 in tap water) were compared in interrupting the transfer of rhinovirus type 14 from stainless steel disks to fingerpads of human volunteers upon a 10-s contact at a pressure of 1 kg/cm2. Ten microliters of the virus, suspended in bovine mucin (5 mg/ml), was placed on each disk, and the inoculum was dried under ambient conditions; the input number on each disk ranged from 0.5 x 10(5) to 2.1 x 10(6) PFU. The dried virus was exposed to 20 microliters of the test disinfectant. The Lysol spray was able to reduce virus infectivity by > 99.99% after a contact of either 1 or 10 min, and no detectable virus was transferred to fingerpads from Lysol-treated disks. The bleach (800 ppm of free chlorine) reduced the virus titer by 99.7% after a contact time of 10 min, and again no virus was transferred from the disks treated with it.(ABSTRACT TRUNCATED AT 250 WORDS)
Novel Method for Identifying Bacterial Mutants with Reduced Epiphytic Fitness
Authors: Lindow Steven E.
Published: January 2020

In order to identify novel traits involved in epiphytic colonization, a technique for the rapid identification of bacterial mutants with quantitatively different population sizes in a natural habitat based on measurements of ice nucleation activity was developed. The threshold freezing temperatures of leaves harboring different numbers of cells of ice nucleation-active
Pseudomonas syringae
B728a differed substantially. While few leaves containing less than about 10
6
cells per g (fresh weight) froze at assay temperatures of -2.75°C or higher, nearly all leaves froze at these temperatures when population sizes of this strain increased to about 10
7
cells per g (fresh weight). Presumptive epiphytic fitness mutants could readily be identified as strains which initiated freezing in fewer leaves than did other strains within a given experiment. Most Tn
5
-induced mutants of strain B728a which conferred a low frequency of ice nucleation on inoculated bean leaves generally had a smaller population size than the parental strain at the time of the leaf freezing assay. The leaf freezing assay was capable of differentiating samples which varied by approximately three- to fivefold in mean bacterial population size.
Biotransformation of polycyclic aromatic hydrocarbons by yeasts isolated from coastal sediments
Authors: MacGillivray A R , Shiaris M P
Published: January 2020

Yeast abundance in the sediments of 13 coastal sites in Massachusetts was quantified, and the potential of yeast isolates to biotransform polycyclic aromatic hydrocarbons (PAHs) was determined. Plate counts of yeasts varied between 10(2) to 10(7) CFU g (dry weight) of sediment-1. The most abundant genera isolated and identified included Candida, Cryptococcus, Rhodotorula, Torulopsis, and Trichosporon. More than 50% of the isolates from heavily contaminated sites transformed phenanthrene, as determined by spray-plate screening. The plate counts of phenanthrene-transforming yeasts correlated significantly to the sediment concentrations of phenanthrene. Transformation of [9-14C]phenanthrene and [12-14C]benz[a]anthracene by individual isolates varied greatly, ranging from 0.15 to 8.15 mumol of PAH g-1 in 120-h incubations. Of the isolated yeasts, Trichosporon penicillatum exhibited the greatest capacity for phenanthrene transformation. The ability to transform PAHs appears to be widespread among yeasts in coastal sediments.
Inactivation of Escherichia coli by titanium dioxide photocatalytic oxidation
Authors: Ireland J C , Klostermann P , Rice E W , Clark R M
Published: January 2020

Titanium dioxide in the anatase crystalline form was used as a photocatalyst to generate hydroxyl radicals in a flowthrough water reactor. Experiments were performed on pure cultures of Escherichia coli in dechlorinated tap water and a surface water sample to evaluate the disinfection capabilities of the reactor. In water devoid of significant amounts of inorganic-radical scavengers, rapid cell death was observed with both pure cultures and members of the indigenous flora in a natural water sample.
Influence of temperature and substrate concentration on bacterial growth yield in Seine River water batch cultures
Authors: Barillier A , Garnier J
Published: January 2020

The growth of natural bacterial assemblages was monitored in 3-liter reactors under various temperature and substrate concentration conditions. The oxygen concentration was continuously monitored, and subsamples were taken at short time intervals to determine bacterial number and biomass. The rate of bacterial mortality was also determined. Bacterial growth yield was calculated as the ratio of net production (increase in biomass corrected for mortality) to gross production (net production plus oxygen consumption expressed in carbon units). Averaging 33%, the growth yield did not show any trend with temperatures in the range of 8 to 25 degrees C but increased with the concentration of dissolved organic carbon in the range of 2 to 12 mg of C.liter-1.
Mineralization of the s-triazine ring of atrazine by stable bacterial mixed cultures
Authors: Mandelbaum R T , Wackett L P , Allan D L
Published: January 2020

Enrichment cultures containing atrazine (2-chloro-4-ethylamino-6-isopropylamino-1,3,5-triazine) at a concentration of 100 ppm (0.46 mM) as a sole nitrogen source were obtained from soils exposed to repeated spills of atrazine, alachlor, and metolachlor. Bacterial growth occurred concomitantly with formation of metabolites from atrazine and subsequent biosynthesis of protein. When ring-labeled [14C]atrazine was used, 80% or more of the s-triazine ring carbon atoms were liberated as 14CO2. Hydroxyatrazine may be an intermediate in the atrazine mineralization pathway. More than 200 pure cultures isolated from the enrichment cultures failed to utilize atrazine as a nitrogen source. Mixing pure cultures restored atrazine-mineralizing activity. Repeated transfer of the mixed cultures led to increased rates of atrazine metabolism. The rate of atrazine degradation, even at the elevated concentrations used, far exceeded the rates previously reported in soils, waters, and mixed and pure cultures of bacteria.
Use of repetitive sequences and the polymerase chain reaction technique to classify genetically related Bradyrhizobium japonicum serocluster 123 strains
Authors: Judd A K , Schneider M , Sadowsky M J , de Bruijn F J
Published: January 2020

We have determined that repetitive (repetitive extragenic palindromic [REP] and enterobacterial repetitive intergenic consensus [ERIC]) sequences used in conjunction with the polymerase chain reaction technique (REP and ERIC PCR) provide an effective means of differentiating between and classifying genetically related Bradyrhizobium japonicum serocluster 123 strains. Analysis of REP and ERIC PCR-generated dendrograms indicated that this technique can effectively differentiate between closely related strains which were indistinguishable by using other classification methods. To maximize the genomic differences detected by REP and ERIC PCR fingerprint patterns, the REP and the ERIC data sets were combined for statistical analyses. REP-plus-ERIC PCR fingerprints were also found to provide a method to differentiate between highly diverse strains of Bradyrhizobium spp., but they did not provide an effective means for classifying these strains because of the relatively low number of REP and ERIC consensus sequences found in some of the bradyrhizobia. Our results also suggest that there is a relationship between nodulation phenotypes and the distribution of REP and ERIC consensus sequences within the genomes of B. japonicum serogroup 123 and 127 strains. Results obtained by restriction fragment length polymorphism hybridization analyses were correlated with the phylogenetic classification of B. japonicum serocluster 123 strains obtained by using REP and ERIC PCR.
Purification and characterization of a thermostable xylanase from Bacillus stearothermophilus T-6
Authors: Khasin A , Alchanati I , Shoham Y
Published: January 2020

Bacillus stearothermophilus T-6 produces an extracellular xylanase that was shown to optimally bleach pulp at pH 9 and 65 degrees C. The enzyme was purified and concentrated in a single adsorption step onto a cation exchanger and is made of a single polypeptide with an apparent M(r) of 43,000 (determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis). Xylanase T-6 is an endoxylanase that completely degrades xylan to xylose and xylobiose. The pIs of the purified protein were 9 and 7 under native and denaturing conditions, respectively. The optimum activity was at pH 6.5; however, 60% of the activity was still retained at pH 10. At 65 degrees C and pH 7, the enzyme was stable for more than 10 h; at 65 degrees C and pH 9, the half-life of the enzyme was approximately 6 h. Kinetic experiments at 55 degrees C gave Vmax and Km values of 288 U/mg and 1.63 mg/ml, respectively. The enzyme had no apparent requirement for cofactors, and its activity was strongly inhibited by Zn2+, Cd2+, and Hg2+. Xylan completely protected the protein from inactivation by N-bromosuccinimide. The N-terminal sequence of the first 45 amino acids of the enzyme showed high homology with the N-terminal region of xylanase A from the alkalophilic Bacillus sp. strain C-125.
Effect of amino acids on the heat production and growth efficiency of Streptococcus bovis: balance of anabolic and catabolic rates
Authors: Russell J B
Published: January 2020

Streptococcus bovis JB1 grew nearly twice as fast (0.9 versus 1.6 h-1) and had a 40% greater growth yield (18 versus 12.5 mg of protein per mmol of glucose) when an ammonia-based medium was supplemented with amino acids, but the glucose consumption rate (88 mumol mg of protein-1 h-1) and specific rate of heat production (2.1 mW/mg of protein) were unaffected. Amino acid availability had little effect on the catabolic rate, but the specific heat decreased 40% (8.8 to 5.2 J/mg of protein). These growth rate-dependent changes in metabolic efficiency were fivefold greater than the maintenance energy. Chloramphenicol (100 mg/l), an inhibitor of protein synthesis, caused a gradual decrease in anabolic (growth) rate, but there was little change in the rate of glucose consumption and the specific heat increased. When growth was inhibited by iodoacetate, the catabolic and anabolic rates both declined and there was not increase in specific heat. On the basis of these results, the benefit of amino acid supplementation was largely explained by the balance of anabolic and catabolic rates. When amino acids were available, the anabolic and catabolic rates were more closely matched and less energy was spilled as heat.
Studies of the Physiological and Genetic Basis of Acid Tolerance in
Rhizobium leguminosarum
biovar trifolii
Authors: Chen Hancai , Richardson Alan E. , Rolfe Barry G.
Published: January 2020

Acid-tolerant
Rhizobium leguminosarum
biovar trifolii ANU1173 was able to grow on laboratory media at a pH as low as 4.5. Transposon Tn
5
mutagenesis was used to isolate mutants of strain ANU1173, which were unable to grow on media at a pH of less than 4.8. The acid-tolerant strain ANU1173 maintained a near-neutral intracellular pH when the external pH was as low as 4.5. In contrast, the acid-sensitive mutants AS25 and AS28 derived from ANU1173 had an acidic intracellular pH when the external pH was less than 5.5. The acid-sensitive
R. leguminosarum
biovar trifolii ANU794, which was comparatively more sensitive to low pH than mutants AS25 and AS28, showed a more acidic internal pH than the two mutants when the three strains were exposed to medium buffered at a pH of less than 5.5. The two acid-sensitive mutants had an increased membrane permeability to protons but did not change their proton extrusion activities. However, the acid-sensitive strain ANU794 exhibited both a higher membrane permeability to protons and a lower proton extrusion activity compared with the acid-tolerant strain ANU1173. DNA hybridization analysis showed that mutants AS25 and AS28 carried a single copy of Tn
5
located in 13.7-kb (AS25) and 10.0-kb (AS28)
Eco
RI DNA fragments. The wild-type DNA sequences spanning the mutation sites of mutants AS25 and AS28 were cloned from genomic DNA of strain ANU1173. Transfer of these wild-type DNA sequences into corresponding Tn
5
-induced acid-sensitive mutants, respectively, restored the mutants to their acid tolerance phenotypes. Mapping studies showed that the AS25 locus was mapped to a 5.6-kb
Eco
RI-
Bam
HI megaplasmid DNA fragment, whilst the AS28 locus was located in an 8.7-kb
Bgl
II chromosomal DNA fragment.
Acid adaptation induces cross-protection against environmental stresses in Salmonella typhimurium
Authors: Leyer G J , Johnson E A
Published: January 2020

The relationship of acid adaptation to tolerance of other environmental stresses was examined in Salmonella typhimurium. S. typhimurium was adapted to acid by exposing the cells to mildly acidic conditions (pH 5.8) for one to two cell doublings. Acid-adapted cells were found to have increased tolerance towards various stresses including heat, salt, an activated lactoperoxidase system, and the surface-active agents crystal violet and polymyxin B. Acid adaptation increased cell surface hydrophobicity. Specific outer membrane proteins were induced by acid adaptation, but the lipopolysaccharide component appeared to be unaltered. These results show that acid adaptation alters cellular resistance to a variety of environmental stresses. The mechanism of acid-induced cross-protection involved changes in cell surface properties in addition to the known enhancement of intracellular pH homeostasis.
Dehydrogenases involved in the conversion of succinate to 4-hydroxybutanoate by Clostridium kluyveri
Authors: Wolff R A , Urben G W , O'Herrin S M , Kenealy W R
Published: January 2020

A pathway of succinate fermentation to acetate and butanoate (butyrate) in Clostridium kluyveri has been supported by the results of 13C nuclear magnetic resonance studies of the metabolic end products of growth and the detection of dehydrogenase activities involved in the conversion of succinate to 4-hydroxybutanoate (succinic semialdehyde dehydrogenase and 4-hydroxybutanoate dehydrogenase). C. kluyveri fermented [1,4-13C]succinate primarily to [1-13C]acetate, [2-13C]acetate, and [1,4-13C]butanoate. Any pathway proposed for this metabolism must account for the reduction of a carboxyl group to a methyl group. Succinic semialdehyde dehydrogenase activity was demonstrated after separation of the crude extracts of cells grown on succinate and ethanol (succinate cells) by anaerobic nondenaturing polyacrylamide gel electrophoresis. 4-Hydroxybutanoate dehydrogenase activity in crude extracts of succinate cells was detected and characterized. Neither activity was found in cells grown on acetate and ethanol (acetate cells). Analysis of cell extracts from acetate cells and succinate cells by sodium dodecyl sulfate-polyacrylamide gel electrophoreses showed that several proteins were present in succinate cell extracts that were not present in acetate cell extracts. In addition to these changes in protein composition, less ethanol dehydrogenase and hydrogenase activity was present in the crude extracts from succinate cells than in the crude extracts from acetate cells. These data support the hypothesis that C. kluyveri uses succinate as an electron acceptor for the reducing equivalents generated from the ATP-producing oxidation of ethanol.
Presence of Culturable Bacteria in Cocoons of the Earthworm
Eisenia fetida
Authors: Zachmann Joseph E. , Molina J. A. E.
Published: January 2020

Viable bacteria were found to coexist with developing embryos in egg capsules (cocoons) of the earthworm
Eisenia fetida
. Earthworms were reared under standardized conditions, and bacterial densities were measured in distinct batches of cocoons collected weekly for 10 weeks. Cocoons weighing 12 mg contained a mean viable bacterial population of approximately 10
8
CFU/g of cocoons. No difference was found in viable counts obtained from cocoons incubated at 15°C and cocoons incubated at 24°C. Viable bacterial numbers increased with cocoon age, while acridine orange direct counts of microbial cells were stable at approximately 10
9
cells per g of cocoons. Bacteria isolated from cocoons were used to develop antisera in rabbits for the production of strain-specific fluorescent antibodies. Fluorescent antibody and selective plating techniques were used to monitor populations of these bacteria in earthworm bedding and to determine whether cocoons acquire bacteria from the environment in which they are formed. Cocoon isolates were readily recovered from cocoons formed in inoculated bedding at densities of 10
8
CFU/g of cocoons.
Bradyrhizobium japonicum
USDA 110 and UMR 161 added to bedding were also recovered from cocoons, but at lower densities than cocoon isolates.
Escherichia coli
K-12(pJP4) inoculum was recovered from bedding but not from cocoons. The bacterial complement of
Eisenia fetida
cocoons is affected by inoculation of selected bacterial isolates in the worm growth environment.
Degradation of phenanthrene, fluorene, fluoranthene, and pyrene by a Mycobacterium sp
Authors: Boldrin B , Tiehm A , Fritzsche C
Published: January 2020

Mycobacterium sp. strain BB1 was isolated from a former coal gasification site. It was able to utilize phenanthrene, pyrene, and fluoranthene as sole sources of carbon and energy and to degrade fluorene cometabolically. Exponential growth with solid phenanthrene, pyrene, and fluoranthene was obtained in fermentor cultures. The growth rates were 0.069, 0.056, and 0.040 h-1, respectively. Several metabolites of phenanthrene and fluorene metabolism were identified.
NAH plasmid-mediated catabolism of anthracene and phenanthrene to naphthoic acids
Authors: Menn F M , Applegate B M , Sayler G S
Published: January 2020

Pseudomonas fluorescens 5R contains an NAH7-like plasmid (pKA1), and P. fluorescens 5R mutant 5RL contains a bioluminescent reporter plasmid (pUTK21) which was constructed by transposon mutagenesis. Polymerase chain reaction mapping confirmed the localization of lux transposon Tn4431 300 bp downstream from the start of the nahG gene. Two degradation products, 2-hydroxy-3-naphthoic acid and 1-hydroxy-2-naphthoic acid, were recovered and identified from P. fluorescens 5RL as biochemical metabolites from the biotransformation of anthracene and phenanthrene, respectively. This is the first report which provides direct biochemical evidence that the naphthalene plasmid degradative enzyme system is involved in the degradation of higher-molecular-weight polycyclic aromatic hydrocarbons other than naphthalene.
Influence of pH and Temperature on Enumeration of Cellulose- and Hemicellulose-Degrading Thermophilic Anaerobes in Neutral and Alkaline Icelandic Hot Springs
Authors: Mathrani Indra M. , Nielsen Peter , Sonne-Hansen Jacob , Kristjánsson Jakob K. , Ahring Birgitte K.
Published: January 2020

Cellulose- and hemicellulose-degrading thermophilic anaerobes were enumerated in biomat samples of various temperatures from two different hot springs in the Hveragerǒi area of Iceland: one spring had a pH near 7, the second had a pH near 9. The most-probable-number technique was used for enumeration of bacteria in the samples, with media at many different temperatures (37 to 90°C) and two pH values (7 and 9). There were generally more xylan-degrading then cellulose-utilizing organisms in both environments. There was no growth at 80°C in the neutral spring or at 37°C in the alkaline spring. However, there were large numbers of both types of organisms in the alkaline spring at 80°C and in the neutral spring at 37°C. No cultures grew from the most-probable-number tubes inoculated with the Hveragerǒi samples and incubated at 90°C or with media at pH 9. However, xylan-degrading cultures at 70°C were enriched at pH 9 with samples from some other Icelandic hot springs.
Transduction of a Plasmid Carrying the Cohesive End Region from
Lactococcus lactis
Bacteriophage ΦLC3
Authors: Birkeland Nils-Kåre , Holo Helge
Published: January 2020

Plasmids carrying the cohesive end region from temperate lactococcal bacteriophage ΦLC3 could be packaged in vivo by ΦLC3 and transduced into its host strain,
Lactococcus lactis
subsp.
cremoris
NCDO 1201. The transduction frequencies were between 10
-4
and 10
-3
transducing particles per PFU, depending on the size of the phage DNA insert. This transduction system is limited to only certain lactococcal strains. The ΦLC3 cohesive site region (
cos
) appears to play an important role in plasmid transduction.
Neutral Red Assay for Measurement of Quantitative Vero Cell Cytotoxicity
Authors: Valdivieso-Garcia A. , Clarke R. C. , Rahn K. , Durette A. , MacLeod D. L. , Gyles C. L.
Published: January 2020

A neutral red assay involving Vero cells was used to quantitate the cytotoxic activity of verotoxins (VT) produced by
Escherichia coli
and to investigate changes in titer caused by altering the composition of the cell culture medium. Three variations on medium 199 were investigated: one involved supplementing the medium with 5% fetal bovine serum (FBS), a second was the use of serum-free (SF) medium that contained 5% bovine serum albumin and 5 μg of fibronectin per ml, and the third involved the use of 4% Ultroser G, a commercial serum replacement. The level of cytotoxicity varied markedly with the type of VT and with the medium that was used. For VT1, there was no difference in cytotoxicity between medium with 5% FBS and SF medium, but cytotoxicity was reduced more than 100-fold in medium containing Ultroser G compared with cytotoxicity in the other media. For VT2, VT2v, and VTe, there was a slight reduction in cytotoxicity in medium containing 4% Ultroser G and a more marked reduction in SF medium compared with cytotoxicity in medium containing 5% FBS.
Mineral Products of Pyrrhotite Oxidation by
Thiobacillus ferrooxidans
Authors: Bhatti Tariq M. , Bigham Jerry M. , Carlson Liisa , Tuovinen Olli H.
Published: January 2020

The biological leaching of pyrrhotite (Fe

1-
x

S) by
Thiobacillus ferrooxidans
was studied to characterize the oxidation process and to identify the mineral weathering products. The process was biphasic in that an initial phase of acid consumption and decrease in redox potential was followed by an acid-producing phase and an increase in redox potential. Elemental S was one of the first products of pyrrhotite degradation detected by X-ray diffraction. Pyrrhotite oxidation also yielded K-jarosite [KFe
3
(SO
4
)
2
(OH)
6
], goethite (α-FeOOH), and schwertmannite [Fe
8
O
8
(OH)
6
SO
4
] as solid-phase products. Pyrrhotite was mostly depleted after 14 days, whereas impurities in the form of pyrite (cubic FeS
2
) and marcasite (orthorhombic FeS
2
) accumulated in the leach residue.
Effects of Grazing by Flagellates on Competition for Ammonium between Nitrifying and Heterotrophic Bacteria in Soil Columns
Authors: Verhagen Frank J. M. , Duyts Hendrik , Laanbroek Hendrikus J.
Published: January 2020

The enhanced mineralization of immobilized nitrogen by bacteriophagous protozoa has been thought to favor the nitrification process in soils in which nitrifying bacteria must compete with heterotrophic bacteria for the available ammonium. To obtain more insight into this process, the influence of grazing by the flagellate
Adriamonas peritocrescens
on the competition for ammonium between the chemolithotrophic species
Nitrosomonas europaea
and the heterotrophic species
Arthrobacter globiformis
in the presence of
Nitrobacter winogradskyi
was studied in soil columns, which were continuously percolated with media containing 5 mM ammonium and different amounts of glucose at a dilution rate of 0.007 h
-1
(liquid volumes).
A. globiformis
won the competition for ammonium. The grazing activities of the flagellates had two prominent effects on the competition between
N. europaea
and
A. globiformis
. First, the distribution of ammonium over the profile of the soil columns was more uniform in the presence of flagellates than in their absence. In the absence of flagellates, relatively high amounts of ammonium accumulated in the upper layer (0 to 3 cm), whereas in the underlying layers the ammonium concentrations were low. In the presence of flagellates, however, considerable amounts of ammonium were found in the lower layers, whereas less ammonium accumulated in the upper layer. Second, the potential ammonium-oxidizing activity of
N. europaea
was stimulated in the presence of flagellates. The numbers of
N. europaea
at different glucose concentrations in the presence of flagellates were comparable to those in the absence of protozoa. However, in the presence of flagellates, the potential ammonium-oxidizing activities were four to five times greater than those in the absence of protozoa.
Fate of Agrobacterium radiobacter K84 in the environment
Authors: Stockwell V O , Moore L W , Loper J E
Published: January 2020

Agrobacterium radiobacter K84 is an effective, commercially applied, biological control agent for the plant disease crown gall, yet little is known about the survival and dissemination of K84. To trace K84 in the environment, spontaneous antibiotic-resistant mutants were used. Growth rates and phenotypes of streptomycin- or rifampin-resistant K84 were similar to those of the parental K84, except the rifampin-resistant mutant produced less agrocin 84 as determined by bioassay. K84 and a strain of Agrobacterium tumefaciens established populations averaging 10(5) CFU/g in the rhizosphere of cherry and persisted on roots for 2 years. K84 established rhizosphere populations between 10(4) and 10(6) CFU/g on cherry, ryegrass, and 11 other herbaceous plants. Populations of K84 declined substantially in fallow soil or water over a 16-week period. K84 was detected in the rhizosphere of ryegrass located up to 40 cm from an inoculum source, indicating lateral dissemination of K84 in soil. In gall tissue on cherry, K84 established populations of 10(5) CFU/g, about 10- to 100-fold less than that of the pathogen. These data demonstrate that K84 persists for up to 2 years in a field environment as a rhizosphere inhabitant or in association with crown gall tissue.
Isolation of Typical Marine Bacteria by Dilution Culture: Growth, Maintenance, and Characteristics of Isolates under Laboratory Conditions
Authors: Schut Frits , de Vries Egbert J. , Gottschal Jan C. , Robertson Betsy R. , Harder Wim , Prins Rudolf A. , Button Don K.
Published: January 2020

Marine bacteria in Resurrection Bay near Seward, Alaska, and in the central North Sea off the Dutch coast were cultured in filtered autoclaved seawater following dilution to extinction. The populations present before dilution varied from 0.11 × 10
9
to 1.07 × 10
9
cells per liter. The mean cell volume varied between 0.042 and 0.074 μm
3
, and the mean apparent DNA content of the cells ranged from 2.5 to 4.7 fg of DNA per cell. All three parameters were determined by high-resolution flow cytometry. All 37 strains that were obtained from very high dilutions of Resurrection Bay and North Sea samples represented facultatively oligotrophic bacteria. However, 15 of these isolates were eventually obtained from dilution cultures that could initially be cultured only on very low-nutrient media and that could initially not form visible colonies on any of the agar media tested, indicating that these cultures contained obligately oligotrophic bacteria. It was concluded that the cells in these 15 dilution cultures had adapted to growth under laboratory conditions after several months of nutrient deprivation prior to isolation. From the North Sea experiment, it was concluded that the contribution of facultative oligotrophs and eutrophs to the total population was less than 1% and that while more than half of the population behaved as obligately oligotrophic bacteria upon first cultivation in the dilution culture media, around 50% could not be cultured at all. During one of the Resurrection Bay experiments, 53% of the dilution cultures obtained from samples diluted more than 2.5 × 10
5
times consisted of such obligate oligotrophs. These cultures invariably harbored a small rod-shaped bacterium with a mean cell volume of 0.05 to 0.06 μm
3
and an apparent DNA content of 1 to 1.5 fg per cell. This cell type had the dimensions of ultramicrobacteria. Isolates of these ultramicrobacterial cultures that were eventually obtained on relatively high-nutrient agar plates were, with respect to cell volume and apparent DNA content, identical to the cells in the initially obligately oligotrophic bacterial dilution culture. Determination of kinetic parameters from one of these small rod-shaped strains revealed a high specific affinity for the uptake of mixed amino acids (

a°
A

, 1,860 liters/g of cells per h), but not for glucose or alanine as the sole source of carbon and energy (

a°
A

, ± 200 liters/g of cells per h). The ultramicrobial strains obtained are potentially a very important part of picoplankton biomass in the areas investigated.
Inhibitory effect against pathogenic and spoilage bacteria of Pseudomonas strains isolated from spoiled and fresh fish
Authors: Gram L
Published: January 2020

The antibacterial effects of 209 Pseudomonas strains isolated from spoiled iced fish and newly caught fish were assessed by screening target organisms in agar diffusion assays. One-third (67 strains) inhibited the growth of one or several of six target organisms (Escherichia coli, Shewanella putrefaciens, Aeromonas sobria, Pseudomonas fluorescens, Listeria monocytogenes, and Staphylococcus aureus), of which S. aureus and A. sobria were the most sensitive. The inhibitory action was most pronounced among the strains producing siderophores, and the presence of iron eliminated the antibacterial effect of two-thirds of the inhibitory strains. Siderophore-mediated competition for iron may explain the inhibitory activity of these strains. All but nine of the inhibiting strains were found to inhibit the growth of 38 psychrotrophic S. putrefaciens strains isolated from spoiling fish and fish products. Siderophore-containing Pseudomonas culture supernatants inhibited growth of S. putrefaciens, as did the addition of iron chelators (ethylenediamine dihydroxyphenylacetic acid [EDDHA]). In particular, Pseudomonas strains isolated from newly caught and spoiled Nile perch (Lates niloticus) inhibited S. putrefaciens. This suggests that microbial interaction (e.g., competition or antagonism) may influence the selection of a microflora for some chilled food products.