Isolation,characterization and growth kinetics of bacteria metabolizing pentachlorophenol

Summary A soil bacterium capable of utilizing pentachlorophenol (PCP) as a sole source of carbon and energy was examined for its morphological, biochemical, cultural, and physiological characteristics. The organism was a member of the coryneform group of bacteria, probably in the genus Arthrobacter. The isolate exhibited a doubling time of 4–5 h while growing on either glucose or PCP as the sole carbon source. The growth rate on PCP was essentially constant between 10–135 mg/l. At higher concentrations of PCP the growth rate was inhibited. The organism was found to be an excellent scavenger of PCP; a Monod saturation constant of 1.12 mg/l was obtained from chemostat measurements.     

Cholesterol-degrading bacteria: isolation,characterization and bioconversion

Agrobacterium sp. M4, a gram negative, motile, oxidase- and catalase-positive bacterium isolated from 410 colonies from soil was found to degrade cholesterol with high efficiency (within 9 days). The first and most probably the main metabolite of cholesterol degradation was detectable on TLC from the second day of incubation, and it was identified as 4-cholestene-3-one. No substances with cyclopentenoperhydrophenanthrene structure was found under U.V. radiation at 256 and 336nm, or by staining with sulphuric acid after 9 days of incubation. Morphological, cultural and biochemical characteristics of the isolate placed it in the genus Agrobacterium although its urease activity was negative. Further investigation on this newly isolated strain is under way.     

Effects of growth medium, inoculum size, and incubation time on culturability and isolation of soil bacteria

Soils are inhabited by many bacteria from phylogenetic groups that are poorly studied because representatives are rarely isolated in cultivation studies. Part of the reason for the failure to cultivate these bacteria is the low frequency with which bacterial cells in soil form visible colonies when inoculated onto standard microbiological media, resulting in low viable counts. We investigated the effects of three factors on viable counts, assessed as numbers of CFU on solid media, and on the phylogenetic groups to which the isolated colony-forming bacteria belong. These factors were inoculum size, growth medium, and incubation time. Decreasing the inoculum size resulted in significant increases in the viable count but did not appear to affect colony formation by members of rarely isolated groups. Some media that are traditionally used for soil microbiological studies returned low viable counts and did not result in the isolation of members of rarely isolated groups. Newly developed media, in contrast, resulted in high viable counts and in the isolation of many members of rarely isolated groups, regardless of the inoculum size. Increased incubation times of up to 3 months allowed the development of visible colonies of members of rarely isolated groups in conjunction with the use of appropriate media. Once isolated, pure cultures of members of rarely isolated groups took longer to form visible colonies than did members of commonly isolated groups. Using these new media and extended incubation times, we were able to isolate many members of the phyla Acidobacteria (subdivisions 1, 2, 3, and 4), Gemmatimonadetes, Chloroflexi, and Planctomycetes (including representatives of the previously uncultured WPS-1 lineage) as well as members of the subclasses Rubrobacteridae and Acidimicrobidae of the phylum Actinobacteria.     

Combination of a urease inhibitor and a plant essential oil to control coliform bacteria, odour production and ammonia loss from cattle waste

AIM: To evaluate urea hydrolysis, volatile fatty acid (VFA) production (odour) and coliforms in cattle waste slurries after a urease inhibitor N-(n-butyl) thiophosphoric triamide (NBPT) and a plant oil component (thymol) were added. METHODS AND RESULTS: Faeces from cattle fed a diet of 70% corn silage and 30% alfalfa haylage, urine and distilled water in the ratio 50 : 35 : 15 were blended at high speed for 1 min. Triplicate aliquots of 750 ml were amended with NBPT plus or minus thymol and reblended for 1 min, and were poured into 1.6 l wide-mouth jars covered 90% with a lid. After 56 days, thymol (2000 mg kg(-1) waste) in combination with NBPT (80 mg kg(-1) waste) retained 5.2 g of an initial 9.2 g of urea in cattle waste slurries, compared with less than 1 g of urea retained when NBPT was the only additive (P < 0.05). Another experiment using excreta from cattle fed 76.25% high moisture corn, 19.25% corn silage and a 4.5% supplement, blended at a low speed, gave a similar response with urea hydrolysis; and the two treatments, thymol alone and thymol in combination with NBPT, reduced VFA production (P < 0.01) and eliminated all coliform bacteria by day 1. A third experiment indicated coliforms disappeared in the no addition treatment after 8 days; however, they were viable at 6.6 x 10(4) CFU g(-1) waste beyond 35 days in the NBPT treatment. CONCLUSIONS: Thymol supplements the effect of NBPT by increasing the inhibitory period for hydrolysis of urea in cattle waste slurries and nitrogen retention in the waste. SIGNIFICANCE AND IMPACT OF THE STUDY: Thymol and NBPT offer the potential to reduce odour and pathogens in cattle manure, and increase the fertilizer value.     

Porphyra cell cultures: isolation,growth and polysaccharide production

A range of cell lines was isolated fromPorphyra umbilicalis L. (Rhodophyta) tissue using a variety of methods, the most successful involving exposure to a limpet acetone powder enzyme extract for 24 h, homogenisation and filtration through a series of polyester meshes. All established lines grew as 0.1–5 mm diameter aggregates in liquid culture; most were stable and have been grown in shake-flask or air-lift culture for periods in excess of 1 yr without reverting to the foliose growth form. An investigation of the medium used to grow these lines indicated that it was not nitrogen-deficient and that the sodium chloride concentration was optimal. The addition of an organic buffer increased the final cell yield. None of these cell lines grew heterotrophically in medium supplemented with a range of fixed carbon sources. The infrared spectra of polysaccharides isolated fromPorphyra aggregates and from tissue grown under identical conditions indicated that the structures of the two isolates were analogous.Presented at the XIIIth International Seaweed Symposium, University of British Columbia, Vancouver, Canada, August 1989.     

Integrated control of growth and differentiation of normal human prokeratinocytes cultured in serum-free medium: Clonal analyses,growth kinetics,and cell cycle studies

The effects of growth factors, hormones, and calcium on the growth and differentiation of secondary cultures of normal human prokeratinocytes, i.e., proliferative keratinocytes, derived from adult or neonatal skin were determined by culture in serum-free basal medium, MCDB 153. Clonal growth was achieved when MCDB 153 was supplemented with either epidermal growth factor (EGF) or bovine pituitary extract (BPE), provided insulin was present. In the absence of insulin, however, both EGF and BPE were required for clonal growth. Using this assay, it was established that colony-forming efficiency is independent of calcium concentrations above 0.03 mM and averages 56%; colony size, however, was influenced by calcium and EGF concentrations. Optimal clonal growth occurred in medium containing 10 ng/ml EGF and 0.3 mM calcium. By contrast, differentiation was enhanced by the combination of low EGF (0.1 ng/ml) and high calcium (2 mM). This suggests that an inverse relationship exists between the growth response (extent of clonal growth) and the differentiation response (extent of differentiation). These results suggest that proliferation and differentiation are regulated in an integrated manner. Detailed kinetic studies and cytofluorimetric and autoradiographic analyses also showed that exponentially growing secondary cultures of adult and neonatal prokeratinocytes have a 24-hour cell generation time with G₁, S, G₂, and M phases of 12, 8, 3, and 1 hours, respectively. In addition, the data show that such cells can be growth arrested in medium that does not induce differentiation and that such a procedure significantly limits the cell's subsequent proliferative potential. Furthermore, prolonged culture of adult (> 30 population doublings) and neonatal prokeratinocytes (> 50 population doublings) is associated with senescence and the G₁ arrest of noncycling cells.     

The response of Culex quinquefasciatus (Diptera: culicidae) to traps baited with carbon dioxide, 1-octen-3-ol, acetone, butyric acid and human foot odour in Tanzania

The responses of Culex quinquefasciatus Say to traps baited with carbon dioxide, 1-octen-3-ol, acetone, butyric acid and human foot odour were studied in the field in Muheza, north-east Tanzania using Counterflow Geometry (CFG) and Centers for Disease Control (CDC) traps. It was found that significantly more C. quinquefasciatus responded to foot odour collected on nylon stockings than to clean nylon stockings (P < 0.05). Significantly more mosquitoes were caught in a CFG trap baited with carbon dioxide than in traps with either human foot odour, acetone or butyric acid. It was also found that in an outdoor situation a carbon dioxide baited CDC unlit trap collected over 12 times more C. quinquefasciatus than an unbaited CDC unlit trap and nine times more mosquitoes than CDC traps baited with 1-octen-3-ol alone (P < 0.05). The number of mosquitoes caught in a CDC trap baited with 1-octen-3-ol did not differ significantly from that of the unbaited CDC trap (P > 0.05). These results indicate that the Afrotropical C. quinquefasciatus respond significantly better to traps baited with carbon dioxide than to either octenol, acetone or butyric acid, and that human foot odour contains stimuli to which C. quinquefasciatus is attracted under field conditions.     

The tubular loop fermentor: Oxygen transfer,growth kinetics and design

Oxygen transfer measurements using a dynamic method and evaluated with an appropriate mathematical model have been made on a tubular loop bioreactor. Correlations of the type used in tank systems are used to describe the influence of power and aeration rate on the mass transfer coefficient. Yeast cultures grown on hydrocarbon and glucose substrates show growth characteristics similar to conventional tank results. Model considerations for large-scale tubular fermentors allow for the prediction of the steady-state oxygen profiles and maximum reactor length. Combination with two-phase flow and oxygen transfer correlations yields a design procedure for commercial scale tubular loop fermentors.     

Cometabolism of chlorinated solvents by nitrifying bacteria: kinetics, substrate interactions, toxicity effects, and bacterial response

Pure cultures of ammonia-oxidizing bacteria, Nitrosomonas europaea, were exposed to trichloroethylene (TCE), 1,1-dichloroethylene (1,1-DCE), chloroform (CF), 1,2-dichloroethane (1,2-DCA), or carbon tetrachloride (CT), in the presence of ammonia, in a quasi-steady-state bioreactor. Estimates of enzyme kinetics constants, solvent inactivation constants, and culture recovery constants were obtained by simultaneously fitting three model curves to experimental data using nonlinear optimization techniques and an enzyme kinetics model, referred to as the inhibition, inactivation, and recovery (IIR) model, that accounts for inhibition of ammonia oxidation by the solvent, enzyme inactivation by solvent product toxicity, and respondent synthesis of new enzyme (recovery). Results showed relative enzyme affinities for ammonia monooxygenase (AMO) of 1,1-DCE approximately TCE > CT > NH(3) > CF > 1,2-DCA. Relative maximum specific substrate transformation rates were NH(3) > 1,2-DCA > CF > TCE approximately 1,1-DCE > CT (=0). The TCE, CF, and 1,1-DCE inactivated the cells, with 1,1-DCE being about three times more potent than TCE or CF. Under the conditions of these experiments, inactivating injuries caused by TCE and 1,1-DCE appeared limited primarily to the AMO enzyme, but injuries caused by CF appeared to be more generalized. The CT was not oxidized by N. europaea while 1,2-DCA was oxidized quite readily and showed no inactivation effects. Recovery capabilities were demonstrated with all solvents except CF. A method for estimating protein yield, the relationship between the transformation capacity model and the IIR model, and a condition necessary for sustainable cometabolic treatment of inactivating substrates are presented. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 54: 520-534, 1997.     

Feeding and growth of the isopod Asellus aquaticus on actinomycetes, considered as model filamentous bacteria

SUMMARY. Asellus aquaticus was fed for 49 days at 15°C on aquatic actinomycetes in the laboratory. Specific growth rates (wet weight) of animals initially 2.5mm in length ranged from 0.85 to 2.33% day⁻¹ on Micromonospora and Streptomyces S2 respectively. Asellus newly released from the brood-pouch (1.0 mm length) had a similar growth rate (2.74% day⁻¹) on Streptomyces S2. The growth rates of animals fed on actinomycetes were lower than those of animals feeding on macroscopic foods such as Elodea and decaying oak leaves, regardless of the initial size of the animal. However, it was concluded that actinomycetes, and by inference bacteria also, could maintain a population, albeit a slow-growing one, in a situation where macroscopic foods are largely absent.
The possible significance of hyphal diameter of micro-organisms in relation to assimilation from them is discussed. In this connection actinomycetes are considered as model filamentous bacteria.     

Effect of whole-plant corn silage treated with lignocellulose-degrading bacteria on growth performance,rumen fermentation,and rumen microflora in sheep

Lignification of cellulose limits the effective utilisation of fibre in plant cell wall. Lignocellulose-degrading bacteria secrete enzymes that decompose lignin and have the potential to improve fibre digestibility. Therefore, this study aimed to investigate the effect of whole-plant corn silage inoculated with lignocellulose-degrading bacteria on the growth performance, rumen fermentation, and rumen microbiome in sheep. Twelve 2-month-old male hybrid sheep (Dorper ♂ × small-tailed Han ♀) were randomly assigned into two dietary groups (n = 6): (1) untreated whole-plant corn silage (WPCS) and (2) WPCS inoculated with bacterial inoculant (WPCSB). Whole-plant corn silage inoculated with bacterial inoculant had higher in situ NDF digestibility than WPCS. Sheep in the WPCSB group had significantly higher average daily gain, DM intake, and feed conversion rate than those in the WPCS group (P < 0.05). Furthermore, higher volatile fatty acid concentrations were detected in WPCSB rumen samples, leading to lower ruminal pH (P < 0.05). The WPCSB group showed higher abundance of Bacteroidetes and lower abundance of Firmicutes in the rumen microbiome than the WPCS group (P < 0.05). Multiple differential genera were identified, with Prevotella being the most dominant genus and more abundant in WPCSB samples. Moreover, the enriched functional attributes, including those associated with glycolysis/gluconeogenesis and citrate cycle, were more actively expressed in the WPCSB samples than in the WPCS samples. Additionally, certain glucoside hydrolases that hydrolyse the side chains of hemicelluloses and pectins were also actively expressed in the WPCSB microbiome. These findings suggested that WPCSB increased NDF digestibility in three ways: (1) by increasing the relative abundance of the most abundant genera, (2) by recruiting more functional features involved in glycolysis/gluconeogenesis and citrate cycle pathways, and (3) by increasing the relative abundance and/or expression activity of the glucoside hydrolases involved in hemicellulose and pectin metabolism. Our findings provide novel insights into the microbial mechanisms underlying improvement in the growth performance of sheep/ruminants. However, the biological mechanisms cannot be fully elucidated using only metagenomics tools; therefore, a combined multi-omics approach will be used in subsequent studies.     

Hyperhalophilic archaeal biofilms: growth kinetics,structure, and antagonistic interaction in continuous culture

Biofilms by the hyperhalophilic archaea Halorubrum sp. and Halobacterium sp. were analyzed, and for the first time the progression of structural features and the developmental parameters of these sessile populations are described. Optical slicing and digital analysis of sequential micrographs showed that their three dimensional structure was microorganism dependent. Biofilms of Halobacterium sp. developed in clusters that covered about 30% of the supporting surface at the interface level and expanded over about 86?±?4 μm in thickness, while Halorubrum sp. biofilms covered less than 20% of the surface and reached a thickness of 41?±?1 μm. The kinetics of growth was lower in biofilms, with generation times of 27?±?1 and 36?±?2 h for Halobacterium sp. and Halorubrum sp., respectively, as compared to 8.4?±?0.3 and 14?±?1 h in planktonic cultures. Differences between microorganisms were also observed at the cell morphology level. The interaction between the two microorganisms was also evaluated, showing that Halobacterium sp. can outcompete already established Halorubrum sp. biofilms by a mechanism that might include the combined action of tunnelling swimmers and antimicrobial compounds.     

Studies on a thermophilic bacillus: its isolation, properties, and temperature coefficient of growth

A thermophilic bacillus with minimal, optimal, and maximal growth temperatures of 40, 64.5, and 72 C, respectively, was isolated from soil. Biochemical and morphological studies place the isolate in group 1 of the classification of Walker and Wolf. After adaption to nitrate broth, the temperature coefficient for growth was found to be 20,400 cal/mol. When the temperature coefficient for growth of the isolate, psychrophilic bacteria, mesophilic bacteria, and a strain of Bacillus stearothermophilus are compared, there is no correlation with optimal temperature. The form of the Arrhenius equation, as used by some workers, is commented on.     

Ammonia production by ruminal microorganisms and enumeration,isolation, and characterization of bacteria capable of growth on peptides and amino acids from the sheep rumen

Excessive NH(3) production in the rumen is a major nutritional inefficiency in ruminant animals. Experiments were undertaken to compare the rates of NH(3) production from different substrates in ruminal fluid in vitro and to assess the role of asaccharolytic bacteria in NH(3) production. Ruminal fluid was taken from four rumen-fistulated sheep receiving a mixed hay-concentrate diet. The calculated rate of NH(3) production from Trypticase varied from 1.8 to 19.7 nmol mg of protein(-1) min(-1) depending on the substrate, its concentration, and the method used. Monensin (5 micro M) inhibited NH(3) production from proteins, peptides, and amino acids by an average of 28% with substrate at 2 mg/ml, compared to 48% with substrate at 20 mg/ml (P = 0.011). Of the total bacterial population, 1.4% grew on Trypticase alone, of which 93% was eliminated by 5 micro M monensin. Many fewer bacteria (0.002% of the total) grew on amino acids alone. Nineteen isolates capable of growth on Trypticase were obtained from four sheep. 16S ribosomal DNA and traditional identification methods indicated the bacteria fell into six groups. All were sensitive to monensin, and all except one group (group III, similar to Atopobium minutum), produced NH(3) at >250 nmol min(-1) mg of protein(-1), depending on the medium, as determined by a batch culture method. All isolates had exopeptidase activity, but only group III had an apparent dipeptidyl peptidase I activity. Groups I, II, and IV were most closely related to asaccharolytic ruminal and oral Clostridium and Eubacterium spp. Group V comprised one isolate, similar to Desulfomonas piger (formerly Desulfovibrio pigra). Group VI was 95% similar to Acidaminococcus fermentans. Growth of the Atopobium- and Desulfomonas-like isolates was enhanced by sugars, while growth of groups I, II, and V was significantly depressed by sugars. This study therefore demonstrates that different methodologies and different substrate concentrations provide an explanation for different apparent rates of ruminal NH(3) production reported in different studies and identifies a diverse range of hyper-ammonia-producing bacteria in the rumen of sheep.     

Brugia pahangi and Wolbachia: the kinetics of bacteria elimination,worm viability,and host responses following tetracycline treatment

Wolbachia spp., first reported from filariae nearly 30 years ago, have been suggested to contribute to the pathogenesis associated with human filarial infection. Tetracycline has been used to cure filariae of Wolbachia, as a novel means of chemotherapeutic treatment for both ocular and lymphatic filariasis. Tetracycline treatment of L4 or adult Brugia pahangi in vivo resulted in Wolbachia clearance. Less tetracycline was required to clear Wolbachia when treatment began at the L4 stage, compared with adults. Female worms died earlier than male worms when tetracycline was administered at the L4 stage. In all cases, Wolbachia clearance was closely associated with worm death. Worm recoveries decreased following the L4-L5 molt, suggesting tetracycline does not interrupt molting in this model system. Despite worm death and the assumed release of both bacterial- and worm-derived molecules, differences in inflammatory cell population and T cell cytokine mRNA profiles were negligible between tetracycline-treated and non-treated B. pahangi infected gerbils. These data suggest the contribution of Wolbachia to the in vivo induction of the gerbil immune response to B. pahangi may be small.     

Phosphate-limited continuous culture of Rhodotorula rubra: kinetics of transport, leakage, and growth.

The phosphate-limited growth kinetics of Rhodotorula rubra, a small yeast of marine origin, were examined by analysis of 32P distributions in continuous cultures. Isotope relaxation procedures were used to identify unidirectional flows of Pi and organic phosphate among compartments modeled during growth. The concentrations of phosphates in these compartments at various growth rates were used, together with attendant flows, to produce a mathematical model of growth. Both Pi and phosphate-containing metabolic intermediates leaked from cells during growth. Total leakage ranged from 4 to 10% of influx and was comprised mostly of Pi. Transport capacity was at least 10 times that required for growth at saturating Pi concentrations, so that influx was linear with concentration during growth. This led to the realization that the curvature of Monod plots (Kmu = 12 nM mumax = 0.18/h, and the threshold At = 2.5 nM) is due to change in yield with growth rate. Growth rate related to Pi by the affinity, aA (= 0.43 liter/mg of cells.h) of cells for Pi and the growth rate-dependent yield. It was also specified by a series of kinetic constants that specified flow among the various compartments and equilibrium compartment concentrations as they were set by extracellular Pi. The importance of leakage by healthy cells to the organic chemistry of aquatic systems is noted.     

Dead flower buds of pear: effect of tree growth control, and Alternaria alternata as causal agent

Dead (dormant) flower buds of pear is an important phenomenon in pear production in the Netherlands. Vigourous or unbalanced tree growth and Pseudomonas syringae pv. syringae are mentioned as likely causes of dead flower buds. Several tree growth control treatments including ethephon. Regalis (Prohexadione-Ca) and root pruning were evaluated. Regalis increased disease incidence. The plant stimulant (foliar fertilizer) Resistim (potassium phosphonate) reduced disease incidence. Pseudomonas syringae pv. syringae was occasionally isolated from diseased flower buds. However, Alternaria alternata was nearly always isolated from diseased buds. Indicating a strong relation between this fungus and dead flower buds of pear.     

Screening for and isolation and identification of malathion-degrading bacteria: cloning and sequencing a gene that potentially encodes the malathion-degrading enzyme,carboxylestrase in soil bacteria

Five malathion-degrading bacterial strains were enriched and isolated from soil samples collected from different agricultural sites in Cairo, Egypt. Malathion was used as a sole source of carbon (50 mg/l) to enumerate malathion degraders, which were designated as IS1, IS2, IS3, IS4, and IS5. They were identified, based on their morphological and biochemical characteristics, as Pseudomonas sp., Pseudomonas putida, Micrococcus lylae, Pseudomonas aureofaciens, and Acetobacter liquefaciens, respectively. IS1 and IS2, which showed the highest degrading activity, were selected for further identification by partial sequence analysis of their 16S rRNA genes. The 16S rRNA gene of IS1 shared 99% similarity with that of Alphaprotoebacterium BAL284, while IS2 scored 100% similarity with that of Pseudomonas putida 32zhy. Malathion residues almost completely disappeared within 6 days of incubation in IS2 liquid cultures. LC/ESI-MS analysis confirmed the degradation of malathion to malathion monocarboxylic and dicarboxylic acids, which formed as a result of carboxylesterase activity. A carboxylesterase gene (CE) was amplified from the IS2 genome by using specifically designed PCR primers. The sequence analysis showed a significant similarity to a known CE gene in different Pseudomonas sp. We report here the isolation of a new malathion-degrading bacteria from soils in Egypt that may be very well adapted to the climatic and environmental conditions of the country. We also report the partial cloning of a new CE gene. Due to their high biodegradation activity, the bacteria isolated from this work merit further study as potential biological agents for the remediation of soil, water, or crops contaminated with the pesticide malathion.     

Investigation of mercaptans,organic sulfides,and inorganic sulfur compounds as sulfur sources for the growth of methanogenic bacteria

A variety of compounds were investigated for use as sulfur sources for the growth of methanogenic bacteria.Methanococcus (Mc.) deltae, Mc. maripaludis, Methanobacterium (Mb.) speciesGC-2B, GC-3B, andMMY, Methanobrevibacter (Mbr.) ruminantium, andMethanosarcina (Ms.) barkeri strain 227 grew well with sulfide, S^o, thiosulfate, or cysteine as sole sulfur source.Mbr. ruminatium was able to grow on SO ₄ ⁼ or SO ₃ ⁼ , andMs. barkeri strain 227 was able to grow on SO ₃ ⁼ , but not on SO ₄ ⁼ as a sole sulfur source.Mc. jannaschii grew with sulfide, S^o, thiosulfate or SO ₃ ⁼ , but not on cysteine or SO ₄ ⁼ as sole surface source.Mc. thermolithotrophicus, Mc. jannaschii, Mc. deltae, andMb. thermoautotrophicum strains Marburg and H were able to grow with methanethiol, ethanethiol,n-propanethiol,n-butanethiol, methyl sulfide, dimethyl sulfoxide, ethyl sulfide, or CS₂ as a sulfur source, when very low levels (20–30 M) of sulfide were present; no growth occurred on 5–100 M sulfide alone. Methanethiol, ethanethiol, and methyl sulfide-using cultures produced sulfide during growth.