Interactions of earthworms with Atrazine-degrading bacteria in an agricultural soil

In the last 10 years, accelerated mineralization of Atrazine (2-chloro-ethylamino-6-isopropylamino-s-triazine) has been evidenced in agricultural soils repeatedly treated with this herbicide. Here, we report on the interaction between earthworms, considered as soil engineers, and the Atrazine-degrading community. The impact of earthworm macrofauna on Atrazine mineralization was assessed in representative soil microsites of earthworm activities (gut contents, casts, burrow linings). Soil with or without earthworms, namely the anecic species Lumbricus terrestris and the endogenic species Aporrectodea caliginosa, was either inoculated or not inoculated with Pseudomonas sp. ADP, an Atrazine-degrading strain, and was either treated or not treated with Atrazine. The structure of the bacterial community, the Atrazine-degrading activity and the abundance of atzA, B and C sequences in soil microsites were investigated. Atrazine mineralization was found to be reduced in representative soil microsites of earthworm activities. Earthworms significantly affected the structure of soil bacterial communities. They also reduced the size of the inoculated population of Pseudomonas sp. ADP, thereby contributing to the diminution of the Atrazine-degrading genetic potential in representative soil microsites of earthworm activities. This study illustrates the regulation produced by the earthworms on functional bacterial communities involved in the fate of organic pollutants in soils.     

Microcolony and biofilm formation as a survival strategy for bacteria

Bacterial communities such as biofilms are widely recognized as being important for survival and persistence of bacteria in harsh environments. Mechanistic models of biofilm growth indicate that the way in which the surface is seeded can effect the morphology of simulated biofilms. Experimental studies indicate that genes which are important for chemotaxis also influence biofilm formation, perhaps by influencing aggregation on a surface. Understanding aggregation and microcolony formation could therefore help clarify factors influencing biofilm formation and illuminate how groups influence the fitness of bacteria. In this paper I develop an individual based model to examine how different behaviors involved in microcolony formation on a surface determine patterns of group sizes and link patterns to bacterial fitness.     

Nonconventional hydrolytic dehalogenation of 1-chlorobutane by dehydrated bacteria in a continuous solid-gas biofilter

Rhodococcus erythropolis NCIMB 13064 and Xanthobacter autotrophicus GJ10 are able to catalyze the conversion of halogenated hydrocarbons to their corresponding alcohols. These strains are attractive biocatalysts for gas phase remediation of polluted gaseous effluents because of their complementary specificity for short or medium and for mono-, di-, or trisubstituted halogenated hydrocarbons (C2-C8 for Rhodococcus erythropolis and C1-C4 for Xanthobacter autotrophicus).After dehydration, these bacteria can catalyze the hydrolytic dehalogenation of 1-chlorobutane in a nonconventional gas phase system under a controlled water thermodynamic activity (a(w)). This process makes it possible to avoid the problems of solubility and bacterial development due to the presence of water in the traditional biofilters.In the aqueous phase, the dehalogenase activity of Rhodococcus erythropolis is less sensitive to thermal denaturation and the apparent Michaelis-Menten constants at 30 degrees C were 0.4 mM and 2.40 micromol min(-1) g(-1) for Km and Vmax, respectively. For Xanthobacter autotrophicus they were 2.8 mM and 0.35 micromol min(-1) g(-1). In the gas phase, the behavior of dehydrated Xanthobacter autotrophicus cells is different from that observed with Rhododcoccus erythropolis cells. The stability of the dehalogenase activity is markedly lower. It is shown that the HCl produced during the reaction is responsible for this low stability. Contrary to Rhodococcus erythropolis cells, disruption of cell walls does not increase the stability of the dehalogenase activity.The activity and stability of lyophilized Xanthobacter autotrophicus GJ10 cells are dependant on various parameters. Optimal dehalogenase activity was determined for water thermodynamic activity (a(w)) of 0.85. A temperature of 30 degrees C offers the best compromise between activity and stability. The pH control before dehydration plays a role in the ionization state of the dehalogenase in the cells. The apparent Michaelis-Menten constants Km and Vmax for the dehydrated Xanthobacter autotrophicus cells were 0.07 (1-chlorobutane thermodynamic activity) and 0.08 micromol min(-1) g(-1) of cells, respectively. A maximal transformation capacity of 1.4 g of 1-chlorobutane per day was finally obtained using 1g of lyophilized Xanthobacter autotrophicus GJ10 cells.     

Synthesis and Secretion of Proteinases by Bacillus intermedius in the Late Stages of Sporulation

In the late stages of sporulation, cells of Bacillus intermedius 3-19 secreted into the medium two proteinases, glutamyl endopeptidase and subtilisin, whose maximum activities were recorded in the 40th and 44th hours of growth, respectively. By estimating -galactosidase activity as a marker of cytoplasmic membrane integrity, it was revealed that the accumulation of these proteinases in the medium was a result of their secretion and not of lysis of the cell envelope. Concentrations of peptone and inorganic phosphate ensuring the maximum production of the enzymes were established. Ammonium ions were shown to inhibit the production of proteinases by the mechanism of repression by nitrogen metabolites.     

Design of a biofilter packed with crab shell and operation of the biofilter fed with leaf mold solution as a nutrient

After measuring toluene adsorption (15.7 mg-toluene/g-material), water holding capacity (18.5%), organic content (53.8%), specific surface area (18.1 m²/g-material), and microbial attachment, crab shells were chosen as the main packing material for a biofilter design. The crab shells, cheap and abundant in the Gangneung area, also have relatively rigid structure, low density, and ability to neutralize acids generated during mineralization of toluene. Since towel scraps have water holding capacity as high as 301.2%, 10% of the total packing was supplemented with them to compensate for low water holding capacity of the crab shells. The biofilter fed with defined chemical medium under 0.8∼1.3 mg/L of inlet toluene concentration and 18 seconds of residence time showed satisfactory removal efficiency of over 97% and 72.8 g/h·m³ of removal capacity. For the purpose of deceasing operation costs, leaf mold solution was tried as an alternative nutrient instead of a defined chemical medium. The removal efficiency and removal capacity were 85% and 56.3 g/h·m³, respectively, using the same inlet toluene concentration and residence time. This research shows the possibility of recycling crab shell waste as packing material for biofilter. In addition, leaf mold was able to serve as an alternative nutrient, which remarkably decreased the operating cost of the biofilter.     

Cation-induced thermal stability of an alkaline protease from a Bacillus sp.

An alkaline protease produced from a Bacillus sp. was stimulated by the metal ions Ca²⁺, Mg²⁺ and Mn²⁺; with Ca²⁺ having the maximum effect. The thermal stability of the enzyme was also enhanced to varying degrees in the presence of these ions.     

Biodegradation and detoxification of nicotine in tobacco solid waste by a Pseudomonas sp.

A Pseudomonas sp. grew with nicotine optimally 3 g l^–1 and at 30 °C and pH 7. Nicotine was fully degraded within 10 h. The resting cells degraded nicotine in tobacco solid waste completely within 6 h in 0.02 m sodium phosphate buffer (pH 7) at maximally 56 mg nicotine h^–1 g dry cell^–1.     

Microbial treatment of a styrene-contaminated air stream in a biofilter with high elimination capacities

A styrene-utilizing mixed microbial culture was isolated and utilized in a biofilter for the biological treatment of a contaminated air stream. Biofilter media consisted of composted wood bark and yard waste. The biofilters were acclimated at 120 s residence time and further evaluated at 60 and 30 s gas residence times. The biofilters received organic loading rates of up to 350 g/m³ h. The styrene volumetric removal rate was a function of the organic loading rate and increased with increasing loading rates. Average volumetric removal rates of 69–118 g/m³ h observed in our studies were higher than reported values for styrene biofilters. Average styrene removal efficiencies ranged from 65% to 75% (maximum 100%). Axial analysis of styrene concentration along the column indicated that the bulk of the styrene removal occurred in the first section of the biofilter. Analyses of the media indicated that the moisture content of the first section (50–55% w/w) was significantly lower than in the second and third sections (65–70% w/w). The pressure drops across the biofilter were low due to the high concentration of large media particles. The total pressure drops were 1–3, 4–6, and 10–16 mm for the 120-, 60-, and 30-s residence time periods, respectively. Journal of Industrial Microbiology & Biotechnology (2001) 26, 196–202. Received 04 March 2000/ Accepted in revised form 25 January 2001     

Mixture design as first step for improved glutaminase production in solid-state fermentation by isolated Bacillus

Aim: Investigation of mixture‐design impact on glutaminase production by isolated Bacillus sp. Methods and Results: An augmented simplex centroid design was used to optimize a three (wheat bran, Bengal gram husk and palm seed fibre) component mixture for glutaminase production. Selected substrate materials showed impact on glutaminase production values at individual level by Bengal gram husk [2789 U gds^?1 (gram dry substrate] and in two‐level combination with wheat bran and Bengal gram husk (maximum of 3300 U gds^?1). Conclusion: Bengal gram husk is the most suitable substrate medium for glutaminase production by Bacillus sp. Maximum glutaminase production is achieved using solid‐substrate mixture at two‐level combinations in the ratio of 66 : 34 for Bengal gram husk and wheat bran, respectively. Significance and Impact of the Study: The present study has significance in large‐scale production of glutaminase at commercial level with the use of multi‐substrate rather than single‐substrate/support material.     

Performance and efficiency of a yeast biofilter for the treatment of a Nigerian fertilizer plant effluent

A biofilter composed of yeasts and cassava peel was used to detoxify fertilizer plant effluent. The biological oxygen demand was reduced on treatment from a range of 1200–1400 mg/l to a range 135–404 mg/l. The ammonia-nitrogen (NH₃–N) and nitrate-nitrogen (NO₃–N) were reduced after treatment from 1000 to 10 mg/l and from 100 to 17.6 mg/l, respectively. The biofilter is simple and easy to handle with high efficiency of 98%.     

一株纤维蛋白溶解酶产生菌的鉴定及其产酶条件初步研究

从亚洲传统发酵食品--虾酱中筛选到一株产纤维蛋白溶解酶能力较强的菌株,通过形态和常规生理生化性质鉴定,发现该菌株与芽孢杆菌属细菌的特征很相近,结合16S rDNA序列分析,构建系统发育树,确定其分类地位,由中国典型培养物保藏中心定名为Bacillus sp.nov.SK006(CCTCC No.M 205071),并优化了发酵培养基组成及培养条件,本研究为该菌株的深入研究和广泛应用提供了理论依据.     

Biodegradation Kinetics of Naphthalene in Soil Medium Using Pleurotus Ostreatus in Batch Mode with Addition of Fibrous Biomass as a Nutrient

The efficiency and kinetics of naphthalene biodegradation in a soil medium using Pleurotus ostreatus (a type of white rot fungus) in batch mode with and without the addition of oil palm fiber (OPF) as a nutrient are evaluated in this study. Three batches are considered in the biodegradation study: (i) control—spiked soil; (ii) spiked soil with fungus; and (iii) spiked soil with both fungus and OPF. Biodegradation is conducted over a period of 22 days for which soil naphthalene concentrations are determined with respect to microwave extraction and high-performance liquid chromatography (HPLC) analysis. The results indicate that inoculation with Pleurotus ostreatus significantly enhances soil naphthalene biodegradation to 84%, which is further enhanced upon the addition of OPF to 98% with respect to the degradation rate. The high carbon content in OPF (>40%) affords it the capacity to be a viable nutrient supplement for Pleurotus ostreatus, thereby enhancing the potential of Pleurotus ostreatus in the biodegradation of polycylic aromatic hydrocarbons (PAHs), and indicating the potential of OPF as a nutrient for PAH biodegradation. A relationship between OPF mass and the biodegradation rate constant has been determined to be linear according to the following equation: k = 0.0429 × OPF + 0.1291.     

Experimental investigation of interactions between the temperature field and biofouling in a synthetic treated sewage stream

Biofouling causes significant losses in efficiency in heat exchangers recovering waste heat from treated sewage. The influence of the temperature field on biofouling was investigated using a flat plate heat exchanger which simulated the channels in a plate and frame unit. The test surface was a 316 stainless steel plate, and a solution of Bacillus sp. and Aeromonas sp. was used as a model process liquid. The test cell was operated under co-current, counter-current, and constant wall temperature configurations, which gave different temperature distributions. Biofouling was monitored via changes in heat transfer and biofilm thickness. The effect of uniform temperature on biofouling formation was similar to the effect of uniform temperature on planktonic growth of the organisms. Further results showed that the temperature field, and particularly the wall temperature, influenced the rate of biofouling strongly. The importance of wall temperature suggests that fouling could be mitigated by using different configurations in summer and winter.     

Kinetics of pure cultures of hydrogen-oxidizing denitrifying bacteria and modeling of the interactions among them in mixed cultures

In this study we report the isolation of four denitrifying bacteria from a batch reactor, where the progress of hydrogenotrophic denitrification was examined. Only three of the strains had the ability to use hydrogen as electron donor. In the present work, kinetic batch experiments were carried out in order to study the dynamic characteristics of pure and defined mixed cultures of hydrogen-oxidizing denitrifying bacteria, under anoxic conditions, in a defined synthetic medium, in the presence of nitrates. Kinetic models were developed and the kinetic parameters were determined from the batch experiments for each bacterium separately. The behavior of mixed cultures and the interactions between the bacteria were described using kinetic models based on the kinetic models developed for each bacterium separately and their predictions were compared with the results from mixed culture experiments. The mathematical models that were developed and validated in the present work are capable of describing the behavior of the bacteria in pure and mixed cultures, and in particular, the kinetics of nitrate and nitrite reduction and cell growth.     

Netropsin stimulates the formation of an extracellular proteinase and suppresses protein turnover in sporulating Bacillus megaterium

Abstract Netropsin stimulated the rate of synthesis of an extracellular metalloproteinase in Bacillus megaterium incubated in a sporulation medium. The antibiotic delayed but did not suppress the decrease in the ability to synthesize the proteinase occurring at later sporulation stages. Netropsin also stimulated the synthesis of the proteinase when added to a growing culture; it inhibited the increase of protein turnover which was switched on between the 2nd and 3rd hour in the sporulating population. No refractile spores were developed during 6 h at 35°C in the antibiotic-treated culture. In the control 60% of sporulating cells were observed under similar conditions.     

Three-way interaction model with switching mechanism as an effective strategy for tracing functionally-related genes

Introduction: Identification of functionally-related genes is an important step in understanding biological systems. The most popular strategy to infer functional dependence is to study pairwise correlations between gene expression levels. However, certain functionally-related genes may have a low expression correlation due to their nonlinear interactions. The use of a three-way interaction (3WI) model with switching mechanism (SM) is a relatively new strategy to trace functionally-related genes. The 3WI model traces the dynamic and nonlinear nature of the co-expression relationship of two genes by introducing their link to the expression level of a third gene.

Areas covered: In this paper, we reviewed a variety of existing methods for tracing the 3WIs. Furthermore, we provide a comprehensive review of the previous biological studies based on 3WI models.

Expert commentary: Comparison of features of these methods indicates that the modified liquid association algorithm has the best efficiency for tracing 3WI between others. The limited number of biological studies based on the 3WI suggests that high computational demand of the available algorithms is a major challenge to apply this approach for analyzing high-throughput omics data.     

Ultra-performance liquid chromatography fingerprint combined with chemometrics as an effective strategy for Dianbaizhu species discrimination

Dianbaizhu a folk medicine used for the treatment of rheumatoid arthritis is made from different species of Gaultheria. The main species is Gaultheria leucocarpa var. yunnanensis but other species are being used as substitutes. The objective was to develop a precise and reproducible method to differentiate among these species. A method was developed by using ultra-performance liquid chromatography in combination with chemometric. The method was validated with relative standard deviations of less than 1.96%.     

AbrB is a regulator of the sigma(W) regulon in Bacillus subtilis

The Bacillus subtilis global regulator AbrB was found to negatively control expression of sigW and genes of the sigma(W) regulon. AbrB bound to DNA regions in the autoregulatory sigW promoter and to some, but not all, of the other sigma(W)-dependent promoters in B. subtilis. Defects in antibiotic resistance properties caused by spo0A mutations are at least partially correlated with AbrB repression of the sigma(W) regulon.