Isolation and Characterization of Diuron-degrading Bacteria from Lotic Surface Water

The bacterial community structure of a diuron-degrading enrichment culture from lotic surface water samples was analyzed and the diuron-degrading strains were selected using a series of techniques combining temporal temperature gradient gel electrophoresis (TTGE) of 16 S rDNA gene V1–V3 variable regions, isolation of strains on agar plates, colony hybridization methods, and biodegradation assays. The TTGE fingerprints revealed that diuron had a strong impact on bacterial community structure and highlighted both diuron-sensitive and diuron-adapted bacterial strains. Two bacterial strains, designated IB78 and IB93 and identified as belonging to Pseudomonas sp. and Stenotrophomonas sp., were isolated and shown to degrade diuron in pure resting cells in a first-order kinetic reaction during the first 24 h of incubation with no 3,4-DCA detected. The percentages of degradation varied from 25% to 60% for IB78 and 20% to 65% for IB93 and for a diuron concentration range from 20 mg/L to 2 mg/L, respectively. It is interesting to note that diuron was less degraded by single isolates than by mixed resting cells, thereby underlining a cumulative effect between these two strains. To the best of our knowledge, this is the first report of diuron-degrading strains isolated from lotic surface water.     

Isolation and Characterization of Methanogenic Bacteria from Landfills

Methanogenic bacteria were isolated from landfill sites in the United Kingdom. Strains of Methanobacterium formicicum, Methanosarcina barkeri, several different immunotypes of Methanobacterium bryantii, and a coccoid methanogen distinct from the reference immunotypes were identified.     

Isolation and Characterization of Coumaphos-Metabolizing Bacteria from Cattle Dip

Coumaphos, an organophosphate insecticide, is used for tick control in cattle dipping vats along the U.S.-Mexican border. Recently, several vats (problem vats) have experienced a loss of efficacy because of microbial degradation. Three morphologically distinct bacteria (designated B-1, B-2, and B-3) that metabolized coumaphos were isolated from enrichment cultures that were initiated from problem vat dip material. In general, amino acids, pyrimidines, and acetate supported growth; carbohydrates were not utilized. Only B-2 required growth factors. In resting cell experiments, coumaphos was hydrolyzed to diethylthiophosphoric acid and chlorferon by all three isolates. Chlorferon was subsequently metabolized by B-1 and B-2 to α-chloro-β-methyl-2,3,4-trihydroxy-trans-cinnamic acid. Only B-1 produced additional metabolites. Experiments with [benzo ring-labeled U-¹⁴C]coumaphos or chlorferon demonstrated that B-1 was capable of both mineralizing and incorporating into biomass the aromatic portion of the molecule. The majority of label, however, was recovered in the form of soluble products, including α-chloro-β-methyl-2,3,4-trihydroxy-trans-cinnamic acid. Although B-1 had the capacity to use chlorferon as a carbon source at low concentrations (100 μg/ml), visible growth at higher concentrations (1,000 μg/ml) was not observed. The addition of 400 μg of chlorferon per ml to B-1 cells in the mid-log phase of growth resulted in complete inhibition of growth, while the addition of 100 to 200 μg of chlorferon per ml resulted in partial inhibition. The growth of B-2 and B-3 was inhibited by 100 μg of chlorferon per ml. These data suggest that, although B-1 and, to a lesser extent, B-2 and B-3 are responsible for the primary degradation of coumaphos, other organisms in the enrichment culture may play a secondary role in coumaphos degradation by removing inhibitory products of coumaphos metabolism.     

Isolation and Characterization of Cellulolytic Bacteria from Activated Sludge

Cellulolytic aerobic bacteria were isolated from activated sludge systems. Of the media tested for enumeration, only filter paper media gave reliable counts. Five isolates were studied further for characterization. It was found that one strain (DK) belonged to the genus Cellulomonas. The other four strains expressed similarity to the genus Pseudomonas. The different characteristics that were studied, however, do not permit them to be identified with any recognized species. Based on certain characters we believe that they are alcaligenes-like pseudomonads.     

Isolation and Characterization of Bacteria from the Baltic Sea

A bacteriological examination was done on samples of water and sediment from three localities in the Baltic. The highest numbers of bacteria were recovered from areas subjected to pollution. The isolates included members of the family Enterobacteria-ceae, the genus Pseudomonas and strains of Aeromonas hydrophila, Alteromonas putrefaciens and some Gram positive bacteria. It is suggested tentatively that H2S production in the black sediments was caused by Alt. putrefaciens. None of the isolates had an absolute requirement for NaCl, although all of them were salt-tolerant to varying degrees, and most were able to grow aerobically at salinities comparable with those found in seawater. Isolates belonging to the family Enterobacteriaceae were, however, unable to grow anaerobically under comparable conditions. Freshwater strains of several genera of the family Enterobacteriaceae and of Aeromonas hydrophila and Aer. sobria displayed salt tolerance identical with that of the Baltic isolates. One strain each of Escherichia coli, Klebsiella pneumoniae and Yersinia enterocolitica survived well during three weeks at 17°C in artificial seawater lacking both carbon and nitrogen sources. These results suggest the need for a re-evaluation of the persistence of potentially pathogenic bacteria in the sea.     

Isolation and Characterization of Polyester-Based Plastics-Degrading Bacteria from Compost Soils

Four potential polyester-degrading bacterial strains were isolated from compost soils in Thailand. These bacteria exhibited strong degradation activity for polyester biodegradable plastics, such as polylactic acid (PLA), polycaprolactone (PCL), poly-(butylene succinate) (PBS) and polybutylene succinate-co-adipate (PBSA) as substrates. The strains, classified according to phenotypic characteristics and 16S rDNA sequence, belonging to the genera Actinomadura, Streptomyces and Laceyella, demonstrated the best polyester- degrading activities. All strains utilized polyesters as a carbon source, and yeast extract with ammonium sulphate was utilized as a nitrogen source for enzyme production. Optimization for polyester-degrading enzyme production by Actinomadura sp. S14, Actinomadura sp. TF1, Streptomyces sp. APL3 and Laceyella sp. TP4 revealed the highest polyester-degrading activity in culture broth when 1% (w/v) PCL (18 U/mL), 0.5% (w/v) PLA (22.3 U/mL), 1% (w/v) PBS (19.4 U/mL) and 0.5% (w/v) PBSA (6.3 U/mL) were used as carbon sources, respectively. All strains exhibited the highest depolymerase activities between pH 6.0–8.0 and temperature 40–60°C. Partial nucleotides of the polyester depolymerase gene from strain S14, TF1 and APL3 were studied. We determined the amino acids making up the depolymerase enzymes had a highly conserved pentapeptide catalytic triad (Gly-His-Ser-Met-Gly), which has been shown to be part of the esterase-lipase superfamily (serine hydrolase).     

Isolation and Characterization of Dehalogenases from 2,2-Dichloropropionate-Degrading Soil Bacteria

Five bacterial strains were isolated from polluted soils capable of degrading 2,2-dichloropropionate. In crude extracts, dehalogenase activity against haloacetates and longer-chained 2-haloalkanoic acids could be detected. Results from activity staining indicated that all bacterial strains expressed a single dehalogenase. In further biochemical characterization, two types of D,L-specific 2-haloalkanoic acid dehalogenases were described, which are different from each other not only in molecular weight and electrophoretic mobility, but also in sensitivity towards thiol reagents. Dehalogenases of these strains have been shown to be inducible and are catalyzing halide hydrolysis with inversion of product configuration. Received: 5 July 1996 / Accepted: 1 August 1996     

Isolation and Characterization of Extremely Thermophilic Bacteria from Hot Springs

In order to investigate the mechanism of microbial growth at elevated temperatures, it was tried to isolate different thermophilic microorganisms from wide origins, such as soils, composts, manure piles and hot spring waters. As the result, 5 strains of extremely thermophilic bacteria, the maximum, the optimum and the minimum temperatures for growth of which were 80, 70~75, and 40°C, respectively, were isolated from Izu-Atagawa hot spring and Beppu hot springs. These bacteria were gram-negative, yellow-pigmented, non-motile and non-sporulating rods of 0.5~0.7 μ in diameter and 2~5 μ in length. They were heterotrophs requiring several amino acids (such as glutamate, aspartate, et al.) and vitamins (such as biotin, folic acid and p-aminobenzoic acid) and grew well at neutral to slight alkali pH. The content of GC pairs of DNAs from the 5 strains was 69~70%, and this seemed to be one of the highest values in bacteria so far known. Among the 5 strains, strain AT–62 was named as Thermus flavus sp. n. AT–62 from its morphological and physiological characteristics. Comparison between Thermus flavus and other extremely thermophilic bacteria as Thermus aquaticus and Flavobacterium thermophilum is described and discussed in reference to classification of extremely thermophilic bacteria.     

Isolation and Characterization of Bacteria from the Swedish West Coast

Most of the bacteria isolated from water and sediment samples from a locality off the west coast of Sweden had an absolute requirement for Na+. On the basis of phenotypic characterization and determination of DNA base composition, the strains could be assigned to the genera Beneckea, Alteromonas and Pseudomonas. Apart from a group of sulphide-forming alteromonads, none of the isolates appeared to be identical with organisms described previously.     

Isolation of an Insertion Sequence from Ralstonia solanacearum Race 1 and Its Potential Use for Strain Characterization and Detection

A new insertion sequence (IS), IS1405, was isolated and characterized from a Ralstonia solanacearum race 1 strain by the method of insertional inactivation of the sacB gene. Sequence analysis indicated that the IS is closely related to the members of IS5 family, but the extent of nucleotide sequence identity in 5′ and 3′ noncoding regions between IS1405 and other members of IS5 family is only 23 to 31%. Nucleotide sequences of these regions were used to design specific oligonucleotide primers for detection of race 1 strains by PCR. The PCR amplified a specific DNA fragment for all R. solanacearum race 1 strains tested, and no amplification was observed with some other plant-pathogenic bacteria. Analysis of nucleotide sequences flanking IS1405 and additional five endogenous IS1405s that reside in the chromosome of R. solanacearum race 1 strains indicated that IS1405 prefers a target site of CTAR and has two different insertional orientations with respect to this target site. Restriction fragment length polymorphism (RFLP) pattern analysis using IS1405 as a probe revealed extensive genetic variation among strains of R. solanacearum race 1 isolated from eight different host plants in Taiwan. The RFLP patterns were then used to subdivide the race 1 strains into two groups and several subgroups, which allowed for tracking different subgroup strains of R. solanacearum through a host plant community. Furthermore, specific insertion sites of IS1405 in certain subgroups were used as a genetic marker to develop subgroup-specific primers for detection of R. solanacearum, and thus, the subgroup strains can be easily identified through a rapid PCR assay rather than RFLP analysis.     

Isolation and Characterization of Phenol-Degrading Denitrifying Bacteria

Phenol is a man-made as well as a naturally occurring aromatic compound and an important intermediate in the biodegradation of natural and industrial aromatic compounds. Whereas many microorganisms that are capable of aerobic phenol degradation have been isolated, only a few phenol-degrading anaerobic organisms have been described to date. In this study, three novel nitrate-reducing microorganisms that are capable of using phenol as a sole source of carbon were isolated and characterized. Phenol-degrading denitrifying pure cultures were obtained by enrichment culture from anaerobic sediments obtained from three different geographic locations, the East River in New York, N.Y., a Florida orange grove, and a rain forest in Costa Rica. The three strains were shown to be different from each other based on physiologic and metabolic properties. Even though analysis of membrane fatty acids did not result in identification of the organisms, the fatty acid profiles were found to be similar to those of Azoarcus species. Sequence analysis of 16S ribosomal DNA also indicated that the phenol-degrading isolates were closely related to members of the genus Azoarcus. The results of this study add three new members to the genus Azoarcus, which previously comprised only nitrogen-fixing species associated with plant roots and denitrifying toluene degraders.     

Isolation and Characterization of Arsenate-Reducing Bacteria from Arsenic-Contaminated Sites in New Zealand

Two environmental sites in New Zealand were sampled (e.g., water and sediment) for bacterial isolates that could use either arsenite as an electron donor or arsenate as an electron acceptor under aerobic and anaerobic growth conditions, respectively. These two sites were subjected to widespread arsenic contamination from mine tailings generated from historic gold mining activities or from geothermal effluent. No bacteria were isolated from these sites that could utilize arsenite or arsenate under the respective growth conditions tested, but a number of chemoheterotrophic bacteria were isolated that could grow in the presence of high concentrations of arsenic species. In total, 17 morphologically distinct arsenic-resistant heterotrophic bacteria isolates were enriched from the sediment samples, and analysis of the 16S rRNA gene sequence of these bacteria revealed them to be members of the genera Exiguobacterium, Aeromonas, Bacillus, Pseudomonas, Escherichia, and Acinetobacter. Two isolates, Exiguobacterium sp. WK6 and Aeromonas sp. CA1, were of particular interest because they appeared to gain metabolic energy from arsenate under aerobic growth conditions, as demonstrated by an increase in cellular growth yield and growth rate in the presence of arsenate. Both bacteria were capable of reducing arsenate to arsenite via a non-respiratory mechanism. Strain WK6 was positive for arsB, but the pathway of arsenate reduction for isolate CA1 was via a hitherto unknown mechanism. These isolates were not gaining an energetic advantage from arsenate or arsenite utilization, but were instead detoxifying arsenate to arsenite. As a subsidiary process to arsenate reduction, the external pH of the growth medium increased (i.e., became more alkaline), allowing these bacteria to grow for extended periods of time.     

Isolation and Characterization of Moderately Halophilic Bacteria from Tunisian Solar Saltern

Bacterial screenings from solar saltern in Sfax (Tunisia) lead to the isolation of 40 moderately halophilic bacteria which were able to grow optimally in media with 5–15% of salt. These isolates were phylogenetically characterized using 16S rRNA gene sequencing. Two groups were identified including 36 strains of Gamma-Proteobacteria (90%) and 4 strains of Firmicutes (10%). The Gamma-Proteobacteria group consisted of several subgroups of the Halomonadaceae (52.5%), the Vibrionaceae (15%), the Alteromonadaceae (10%), the Idiomarinaceae (7.5%), and the Alcanivoracaceae (5%). Moreover, three novel species: 183ZD08, 191ZA02, and 191ZA09 were found, show <97% sequence similarity of the 16S rRNA sequences while compared to previously published cultivated species. Most of these strains (70%) were able to produce hydrolases: amylases, proteases, phosphatases, and DNAases. Over the isolates, 60% produced phosphatases, 15.0% proteases, 12.5% amylases and DNAases equally. This study showed that the solar saltern of Sfax is an optimal environment for halophilic bacterial growth, where diverse viable bacterial communities are available and may have many industrial applications.     

Isolation and Selection of Potential Probiotic Bacteria from the Pig Gastrointestinal Tract

The present study aimed to isolate bacterial strains from the pig gastrointestinal tract that have antagonistic activity against potential pathogens and are able to produce antimicrobial compounds. That ability would be a first requirement for the strains’ possible use as probiotics. Samples obtained from pig intestinal mucosa and contents were screened for the presence of antagonistic activity against pathogenic indicator strains of Escherichia coli, Salmonella, and Listeria by means of the double-layer technique. Samples displaying the largest inhibitory halos were further studied for the production of inhibitory substances using the agar diffusion and microtitration methods. The three most promising isolates were identified by sequencing of the 16S rRNA gene and showed highest affiliation to Lactobacillus salivarius. Optimal growth conditions and bacteriocin production were recorded in de Man, Rogosa, and Sharpe broth under anaerobic conditions at 37 °C. The antimicrobial substances were found to be sensitive to proteolytic enzymes but showed good stability at pH values below 6. Our findings suggest that these three intestinal strains are able to produce antimicrobial substances capable of inhibiting the growth of potential enteric pathogens and might have potential as probiotic feed additives for the prevention of gastrointestinal diseases.     

Isolation and Characterization of Rumex acetosa-Associated Mineral-Weathering Bacteria

A total of 121 bacterial strains were isolated from the rhizosphere soils, root and stem interiors of Rumex acetosa to characterize the microenvironment-related changes in the mineral-weathering effectiveness, weathering mechanisms and populations of the bacteria. Among the 121 bacterial strains, 118 bacterial strains were found to weather biotite. The relative abundance of the highly effective mineral-weathering bacteria was different among the rhizosphere soils, root and stem interiors. Notably, the highest and lowest relative abundances of the highly effective mineral-weathering bacteria were observed in the stem and root interiors, respectively. Furthermore, the relative abundance of the highly acid-producing bacteria was significantly higher in the rhizosphere soils and stem interiors, while the highest and lowest relative abundances of the highly siderophore-producing bacteria were found in the stem interiors and rhizosphere soils, respectively. The mineral-weathering bacteria from the rhizosphere soils, root and stem interiors were affiliated with 11, 7 and 4 genera, respectively. In addition, 25–73% of the bacterial genera were specific to the plant-associated environments. The results showed diverse mineral-weathering bacteria in the plant-associated environments and microenvironment-related changes in weathering effectiveness and pattern and populations of the mineral-weathering bacteria. The results also suggested the different biotite-weathering mechanisms used by the bacteria among the plant-associated environments.     

Isolation and Characterization of Halotolerant Alkaliphilic Methanotrophic Bacteria from Tuva Soda Lakes

Two strains (5Z and 20Z) of halotolerant alkaliphilic obligate methanotrophic bacteria were first isolated from moderately saline soda lakes in Tuva (Central Asia). The strains grow fastest at pH 9.0–9.5 and much more slowly at pH 7.0. No growth occurred at pH ≤ 6.8. They require NaHCO₃ or NaCl for growth in alkaline medium. Gram-negative, motile rods with ordered cup-shaped cell wall structures and Type I intracytoplasmic membranes assimilate methane and methanol via the ribulose monophosphate pathway. The G + C content of strains 5Z and 20Z are 47.6 and 47.9 mol%, respectively. Based on their alkaliphilic physiology, both strains were referred to as Methylobacter alcaliphilus sp. nov. The changes in cell phospholipids, fatty acids, and amino acids have been observed upon varying salinity and pH of the medium, thus suggesting structure-function osmoadaptation of the strains studied. Whole-cell experiments revealed the salt- and pH-dependence of CH₄ oxidation and assimilation rates. Cell motility was also Na⁺ dependent and sensitive to some energy uncouplers and ionophores. Received: 7 March 1997 / Accepted: 14 April 1997     

Isolation and Characterization of Polymeric Galloyl-Ester-Degrading Bacteria from a Tannery Discharge Place

The culturable bacteria colonizing the rhizosphere of plants growing in the area of discharge of a tannery effluent were characterized. Relative proportions of aerobic, denitrifying, and sulfate-reducing bacteria were determined in the rhizosphere of Typha latifolia, Canna indica, and Phragmites australis. Aerobic bacteria were observed to be the most abundant group in the rhizosphere, and plant type did not seem to influence the abundance of the bacterial types analyzed. To isolate bacteria able to degrade polyphenols used in the tannery industry, enrichments were conducted under different conditions. Bacterial cultures were enriched with individual polyphenols (tannins Tara, Quebracho, or Mimosa) or with an undefined mixture of tannins present in the tannery effluent as carbon source. Cultures enriched with the effluent or Tara tannin were able to degrade tannic acid. Six bacterial isolates purified from these mixed cultures were able to use tannic acid as a sole carbon source in axenic culture. On the basis of 16S ribosomal DNA sequence analysis, these isolates were closely related to organisms belonging to the taxa Serratia, Stenotrophomonas maltophilia, Klebsiella oxytoca, Herbaspirillum chlorophenolicum, and Pseudomonas putida.     

Isolation and Characterization of Bile Acid 7-Dehydroxylating Bacteria from Human Feces

Methods for isolation of fecal 7α-dehydroxylating bacteria are presented. A total of 219 strains were isolated from feces of healthy humans, and their ability to 7-dehydroxylate cholic, chenodeoxycholic, and ursodeoxycholic acids were examined. Of all the isolates, 14 strains were found to be capable of eliminating the hydroxy group at C-7α and/or C-7β. All the isolates were strictly anaerobic, Gram-positive rods. Thirteen isolates were non-sporeforming bacteria showing certain saccharolytic properties with the production of acid and gas from dextrose, and were catalase-positive but indole-, lecithinase-, urease- and oxidase-negative. Based on the data available at present, it was concluded that they could be regarded as members of the genus Eubacterium. One strain, however was identified as Clostridium sordellii. The isolated strains capable of 7α-dehydroxylating cholic acid and chenodeoxycholic acid were also able to oxidize the hydroxy group at C-7α. Nine strains (10, 12, 36S, M-2, M-17, M-18, Y-98, Y-1112, and Y-1113) of the 7α-dehydroxylating bacteria were confirmed to have 7β-dehydroxylation ability, but five strains (O-51, O-52, O-71, O-72, and Y-67) could not transform ursodeoxycholic acid to lithocholic acid.     

Isolation and Characterization of Toxic Cyanobacteria from Different Natural Sources

We isolated seven algologically and five bacteriologically pure cultures of toxin-producing cyanobacteria from Turgen gorge (Kazakhstan), Karlovy Vary (Czech Republic), and Shar-Nuur Lake, Bayan Ulgiiregion (Mongolia) springs. According to the Daphnia magna test, Desertifilum sp. and Nostoc sp. strains were the most toxic in the test of isolated strains (complete death of all test organisms was detected after 48 h). These strains possessed the highest inhibitory effect on proliferation of the HeLa cancer cell line. The Anabaena sp. 35 and Nostoc sp. 4 strains were also high toxic. Model strains Synechocystis PCC 6803 and Synechococcus elongates PCC 7942, as well as the strain isolated in the present work, Synechococcus sp. 55, were less toxic. Mass spectrometry made it possible to assign cyanobacterial toxins to cyclic depsipeptides. Two cyclic depsipeptides, micropeptin T and oscillapeptin, were detected in Desertifilum sp. extracts. Cryptophycin and small amounts of cyclic depsipeptide micropeptin SD were detected in Nostoc sp. extract.