Effect of pesticides on soil microbial community.

According to guidelines for the approval of pesticides, information about effects of pesticides on soil microorganisms and soil fertility are required, but the relationships of different structures of pesticides on the growth of various groups of soil microorganisms are not easily predicted. Some pesticides stimulate the growth of microorganisms, but other pesticides have depressive effects or no effects on microorganisms. For examples, carbofuran stimulated the population of Azospirillum and other anaerobic nitrogen fixers in flooded and non-flooded soil, but butachlor reduced the population of Azospirillum and aerobic nitrogen fixers in non-flooded soil. Diuron and chlorotoluron showed no difference between treated and nontreated soil, and linuron showed a strong difference. Phosphorus(P)-contains herbicides glyphosate and insecticide methamidophos stimulated soil microbial growth, but other P-containing insecticide fenamiphos was detrimental to nitrification bacteria. Therefore, the following review presents some data of research carried out during the last 20 years. The effects of twenty-one pesticides on the soil microorganisms associated with nutrient and cycling processes are presented in section 1, and the applications of denaturing gradient gel electrophoresis (DGGE) for studying microbial diversity are discussed in section 2.

Analysis of antibiotic fungicide kasugamycin in irrigation water by high performance liquid chromatography.

A high performance liquid chromatographic (HPLC) analysis method with an ultraviolet (UV) detector and an Aqua C18 (250 x 4.6 mm, Phenomenex) column were applied to analyze the antibiotic fungicide kasugamycin in water. An aromatic sulfonic acid spe column (Backerbond, J. T. Backer) was used to remove the interfering materials from irrigation water. A good linear relation existed between the concentration of the fungicide and the peak area, and correlation coefficient of linearity from 0.1 to 10.2 microg/mL was 0.998. The accuracies expressed as the recoveries of kasugamycin from irrigation water ranged from 112.2 to 111.7 %. The precisions expressed as relative standard deviations (RSD) were found to be below 7.0 %. The quantitative detection limit (LOQ) of kasugamycin in irrigation water was set at 2.2 microg/mL which was 2-times higher than the method detection limit (MDL) 1.03 microg/mL. Electrospray ionization-mass (ESI-MS) and fast-atom bombardment-mass (FAB-MS) were applied to compare the ability of identifying the component of the eluent peak from HPLC, and the result indicated that electrospray ionization-mass (ESI-MS) was more sensitive than fast-atom bombardment-mass (FAB-MS) in the detection of kasugamycin. There was no kasugamycin residue detected in irrigation water samples collected from paddyfields at Wufong, indicated that the residues of kasugamycin in water were less than 2.2 microg/mL, and the risk of water contamination was very low.

Exposure effect of fungicide kasugamycin on bacterial community in natural river sediment.

The degradation of kasugamycin in water and the effects of kasugamycin on the bacterial communities in sediment and overlying water were analyzed over a 30-day period. Kasugamycin is generally regarded as nontoxic to microorganisms, but in this study we demonstrated that kasugamycin inhibited the growth of some aquatic bacteria but also stimulated the growth of other resistant bacteria. Microcosms were contaminated with kasugamycin at the 168.4 mg/L (700 times field application rate), and 1462.9 mg/L (6000 times field application rate). The percentages of kasugamycin degraded after 30 days of exposure were 34.1%, and 12.1% in the overlying water treated with 168.4 mg/L and 1462.9 mg/L, respectively. The degradation rates of kanamycin after 30 days of exposure were 1.92 mg/L/day for 164.8 mg/L treated water and 5.88 mg/L/day for 1462.9 mg/L treated water. Degradation rate of kasugamycin in overlying water was associated with an increase in the concentration of kasugamycin. Comparison of DGGE (denaturing gradient gel electrophoresis) profiles showed that the bacterial communities in treated microcosms were varied. Certain species were eliminated whereas some species were stimulated by the application of kasugamycin. The DGGE profiles and UPGMA (unweighted pair-group method using arithmetic averages) dendrograms revealed that the bacterial communities were more complex in treated sediment than in treated overlying water.

Extraction of DNA from soil for analysis of bacterial diversity in transgenic and nontransgenic papaya sites.

The influence of transgenic crops on the soil diversity of microorganisms is one of the major risk assessments being conducted in Taiwan since 2007, and a reliable soil DNA extraction method for denaturing gradient gel electrophoresis (DGGE) is required. Six soils of different type, organic matter content, cation exchange capacity, and pH were tested, and four previously reported soil DNA extraction methods were applied to these soils. Soil DNA extracts by Zhou's CS method plus QIAquick gel was recommended in our laboratory for DGGE to monitor the microbial diversity in soil. There were some differences on the bacterial diversity based on DGGE patterns at the beginning of planting, and the difference decreased after six months. The results also indicated that clay content (10.8-25.0%) and pH (4.4-6.9) of different soil samples we tested did not affect the DNA extraction efficiencies, but positive correlations were found between the organic matter content (1.2-3.9%) of soils and the DNA yields in Widmer's GS method (r = 0.93, p = 0.005) and the MoBio UC method (r = 0.92, p = 0.007). Coefficient of determinations between organic matter content and DNA yield were higher than those between clay content, CEC, and pH, indicating that organic matter content was more correlated with DNA yield than that clay content, CEC, and pH in our soil samples tested.

Effects of lactose and glucose on production of itaconic acid and lovastatin by Aspergillus terreus ATCC 20542.

Fermentation products of Aspergillus terreus ATCC 20542 (a parent strain for lovastatin production) were collected, and the coexistence of itaconic acid (IA) with lovastatin was confirmed in this study. Using a lactose-based medium (LBM), lovastatin production was 873 mg/l on day 10, but IA production was only 22-28 mg/l during the cultures. When lactose in LBM was simply replaced with glucose, IA production was markedly enhanced by 20-fold (491 mg/l on day 5), which showed a growth-associated pattern. The findings indicated that the carbon source used (glucose or lactose) controlled the biosynthetic pathway. The net yield of lovastatin production when using lactose was calculated to be 25.1 mg/g (5.1-fold) in comparison with when using glucose in the cultures. Furthermore, lovastatin production was further increased by 9.2% when IA (0.5 g/l) was added to LBM. When IA was added at 5 g/l, the fermentation broth turned dark-brown, and lovastatin production was reduced by 18.0%. Hence, these two metabolites (IA and lovastatin) produced by the fungus might be related.

Use of real-time polymerase chain reaction (PCR) and transformation assay to monitor the persistence and bioavailability of transgenic genes released from genetically modified papaya expressing nptII and PRSV genes in the soil.

Soil samples were collected from an isolated field from December 2003 to April 2004 where transgenic papaya were planted, and the persistences of transgenic genes of 796 bp (located between 35S promoter and coat protein, 35S-P/PRSV-CP), 398 bp (located between plasmid pBI121 and NOS terminator, pBI121/NOS-T), and 200 bp (located between NOS promoter and nptII gene, NOS-P/nptII) were studied. At the end of planting, the residues of 398 bp in the soil was 0.06 microg g(-1) of soil, whereas the residues of 769 and 200 bp were less than 30 pg g(-1) of soil (detection limit). Kinetics studies on the persistence of these three fragments in sterile distilled water and nonsterile soil microcosms showed that two mechanisms might be involved: an initial fast exponential degradation pattern in the first week and then followed by a slow-release pattern throughout the experiment. Persistence of transgenic DNA in sterile water was longer than in nonsterile soil microcosms, indicating that enzymatic degradation and soil adsorption played important roles on the persistence of DNA in the environment. The reason for the fragment of 398 bp persisted longer than fragments of 769 and 200 bp is not clear, but the guanine plus cytosin (G plus C) content in the DNA fragment might be involved in the stability of DNA in the environment. Biological availability of soil DNA to bacteria conducted by the transformation assay indicated that gene transformation from soil DNA extracts to two Acinetobacter spp. did not occur.

Paenibacillus taiwanensis sp. nov., isolated from soil in Taiwan.

Among a large collection of Taiwanese soil isolates, a novel Gram-variable, rod-shaped, motile and endospore-forming bacterial strain, designated G-soil-2-3(T), was isolated from farmland soil in Wu-Feng, Taiwan. The isolate was subjected to a polyphasic study including 16S rRNA gene sequence analysis, DNA-DNA hybridization experiments, fatty acid analysis and comparative phenotypic characterization. 16S rRNA gene sequence analysis indicated that the organism belongs within the genus Paenibacillus. It contained menaquinone MK-7 as the predominant isoprenoid quinone and anteiso-C(15 : 0) (40.5 %), iso-C(15 : 0) (13.1 %), iso-C(16 : 0) (10.8 %) and anteiso-C(17 : 0) (7.3 %) as the major fatty acids. Phylogenetically, the closest relatives of strain G-soil-2-3(T) were the type strains of Paenibacillus assamensis, Paenibacillus alvei and Paenibacillus apiarius, with 16S rRNA gene sequence similarity of 95.7, 95 and 95.2 %, respectively. DNA-DNA hybridization experiments showed levels of relatedness of 2.8-9.0 % of strain G-soil-2-3(T) with these strains. The G+C content of the DNA was 44.6 mol%. Strain G-soil-2-3(T) was clearly distinguishable from P. assamensis, P. alvei and P. apiarius and thus represents a novel species of the genus Paenibacillus, for which the name Paenibacillus taiwanensis sp. nov. is proposed. The type strain is G-soil-2-3(T) (=BCRC 17411(T)=IAM 15414(T)=LMG 23799(T)=DSM 18679(T)).

Chryseobacterium taiwanense sp. nov., isolated from soil in Taiwan.

Among a large collection of Taiwanese soil isolates, a novel Gram-negative, rod-shaped, non-spore-forming, yellow-pigmented bacterial strain, Soil-3-27(T), was isolated from farmland soil in Wu-Feng, Taiwan. The isolate was subjected to a polyphasic study including 16S rRNA gene sequencing, DNA-DNA hybridization, fatty acid analysis and comparative phenotypic characterization. The 16S rRNA gene sequence analysis indicated that the organism belongs to the genus Chryseobacterium. The organism contains menaquinone MK-6 as the predominant isoprenoid quinone and 15 : 0 iso (43 %), 17 : 1 isoomega9c (17.5 %) and 17 : 0 iso 3-OH (16.6 %) as the major fatty acids. Phylogenetically, the closest relatives of strain Soil-3-27(T) are Chryseobacterium daecheongense, Chryseobacterium defluvii and Chryseobacterium taichungense with 96.7-97.2 % sequence similarity. DNA-DNA hybridization showed relatedness values of 8.5-24.2 % with these species. The DNA G+C content is 36.8 mol%. Strain Soil-3-27(T) is clearly distinguishable from other Chryseobacterium species and represents a novel species, for which the name Chryseobacterium taiwanense sp. nov. is proposed. The type strain is strain Soil-3-27(T) (=BCRC 17412(T)=IAM 15317(T)=LMG 23355(T)).