Quantitative improvement of 16S rDNA DGGE analysis for soil bacterial community using real-time PCR

Treatment of petroleum hydrocarbon contaminated soil by combination of electro-Fenton and biosurfactant-assisted bioslurry process

Removing petroleum hydrocarbons (PHCs) from polluted soil is challenging due to their low bioavailability and degradability. In this study, an experiment was carried out to treat soil polluted with petroleum hydrocarbon using a hybrid electro-Fenton (with BDD anode electrode) and biological processes stimulated with long-chain rhamnolipids (biosurfactants). Electro-Fenton treatment was applied as a pretreatment before the biological process to enhance PHC biodegradability, which would benefit the subsequent biological process. The effects of initial pH, hydroxide concentration, soil organic matter composition, PHCs intermediates during the electro-Fenton process, and total numbers of bacteria in the biological process were analyzed to determine the optimum conditions. The results showed that the optimized electrolysis time for the electro-Fenton was 12 h. The change induced during pretreatment at a specified time was found suitable for the biological process stage and led to 93.6% PHC degradation in combination with the electro-Fenton-and-biological process after 72 h. The combined system's performance was almost 40% higher than individual electro-Fenton and biological treatments. GC-MS analysis confirms the formation of 9-octadecen-1-ol (Z), 2-heptadecene, 1-nonadecene, 1-heneicosene, and pentacosane as fragmentation during the PHCs degradation process. Thus, the electro-Fenton process as pretreatment combined with a biological process stimulated with rhamnolipids (biosurfactants) could be effectively applied to remediate soil polluted with PHCs. However, the system needs further research and investigation to optimize electrolysis time and biosurfactant dose to advance this approach in the soil remediation process.

Molecular Analysis of Soil Bacterial Community Structures for Environmental Risk Assessment with Varieties of Genetically Modified Soybean and Hot Pepper

With the advance in gene technology, genetically modified (GM) crops have increased in recent years. GM crops offer us various benefits. However, there are potential risks of GM crops for the environment. In this study, the impacts of transgenic plants on soil microbial community structures were assessed. Two varieties of soybean (Glycine max L.) and hot pepper (Capsicum annuum L.), which introduced the herbicide-resistant gene, bar, were used in this study. The effects of GM crops on soil microbial community structures were investigated using a cultural method, the denaturing gradient gel electrophoresis (DGGE) procedure, and 16S rRNA gene sequencing on the Illumina platform. Additionally, the persistence of transgenes was monitored using a quantitative real-time PCR procedure. The cultural method, DGGE analysis, and the amplicon-based community profile indicated that soil microbial communities were not significantly different between GM and non-GM lines. The level of the bar gene in GM soybean plots greatly increased when the crops were actively growing, but thereafter gradually decreased to the initial level. Meanwhile, the level of the bar gene in GM hot pepper plots repeatedly increased and decreased according to the flowering stages. These results indicated that soil microbial community structures were not significantly affected.

External and semi-internal controls for PCR amplification of homologous sequences in mixed templates

In a mixed template, the presence of homologous target DNA sequences creates environments that almost inevitably give rise to artifacts and biases during PCR. Heteroduplexes, chimeras, and skewed template-to-product ratios are the exclusive attributes of mixed template PCR and never occur in a single template assay. Yet, multi-template PCR has been used without appropriate attention to quality control and assay validation, in spite of the fact that such practice diminishes the reliability of results. External and internal amplification controls became obligatory elements of good laboratory practice in different PCR assays. We propose the inclusion of an analogous approach as a quality control system for multi-template PCR applications. The amplification controls must take into account the characteristics of multi-template PCR and be able to effectively monitor particular assay performance. This study demonstrated the efficiency of a model mixed template as an adequate external amplification control for a particular PCR application. The conditions of multi-template PCR do not allow implementation of a classic internal control; therefore we developed a convenient semi-internal control as an acceptable alternative. In order to evaluate the effects of inhibitors, a model multi-template mix was amplified in a mixture with DNAse-treated sample. Semi-internal control allowed establishment of intervals for robust PCR performance for different samples, thus enabling correct comparison of the samples. The complexity of the external and semi-internal amplification controls must be comparable with the assumed complexity of the samples. We also emphasize that amplification controls should be applied in multi-template PCR regardless of the post-assay method used to analyze products.

The effects of different disease-resistant cultivars of banana on rhizosphere microbial communities and enzyme activities

To understand the mechanism of soil microbial ecosystem and biochemical properties in suppressing soilborne plant diseases, the relationship between the soil rhizosphere microbial communities, hydrolase activities, and different disease-resistant cultivars was investigated. There were statistically significant differences in microbial diversity in the rhizosphere soil between the disease-tolerant cultivar Fj01 and susceptible cultivar Baxi. The rhizosphere soil of Fj01 showed a trend of higher microbial diversity than that of Baxi. At the same growth stage, the similar trends of variation in microbial community diversity between the two different cultivars were observed. The bacterial community abundance in rhizosphere soil from the two banana cultivars was quantified by real-time PCR assays. The size of the rhizosphere bacterial population from the Fj01 was significantly larger than that from the Baxi during the growing stage from July to September. The activities of urease and phosphatase were analyzed to study the effects of the two banana cultivars to soil ecosystem functioning. Urease activity was significantly higher in the rhizosphere soil of Fj01 than that of Baxi in the period from July to September. However, phosphatase activity showed no significant difference between the two different rhizosphere soils.

Analysis of artifacts suggests DGGE should not be used for quantitative diversity analysis

PCR-denaturing gradient gel electrophoresis (PCR-DGGE) is widely used in microbial ecology for the analysis of comparative community structure. However, artifacts generated during PCR-DGGE of mixed template communities impede the application of this technique to quantitative analysis of community diversity. The objective of the current study was to employ an artificial bacterial community to document and analyze artifacts associated with multiband signatures and preferential template amplification and to highlight their impacts on the use of this technique for quantitative diversity analysis. Six bacterial species (three Betaproteobacteria, two Alphaproteobacteria, and one Firmicutes) were amplified individually and in combinations with primers targeting the V7/V8 region of the 16S rRNA gene. Two of the six isolates produced multiband profiles demonstrating that band number does not correlate directly with α-diversity. Analysis of the multiple bands from one of these isolates confirmed that both bands had identical sequences which lead to the hypothesis that the multiband pattern resulted from two distinct structural conformations of the same amplicon. In addition, consistent preferential amplification was demonstrated following pairwise amplifications of the six isolates. DGGE and real time PCR analysis identified primer mismatch and PCR inhibition due to 16S rDNA secondary structure as the most probable causes of preferential amplification patterns. Reproducible DGGE community profiles generated in this study confirm that PCR-DGGE provides an excellent high-throughput tool for comparative community structure analysis, but that method-specific artifacts preclude its use for accurate comparative diversity analysis.

Decline in topsoil microbial quotient, fungal abundance and C utilization efficiency of rice paddies under heavy metal pollution across South China

Agricultural soils have been increasingly subject to heavy metal pollution worldwide. However, the impacts on soil microbial community structure and activity of field soils have been not yet well characterized. Topsoil samples were collected from heavy metal polluted (PS) and their background (BGS) fields of rice paddies in four sites across South China in 2009. Changes with metal pollution relative to the BGS in the size and community structure of soil microorganisms were examined with multiple microbiological assays of biomass carbon (MBC) and nitrogen (MBN) measurement, plate counting of culturable colonies and phospholipids fatty acids (PLFAs) analysis along with denaturing gradient gel electrophoresis (DGGE) profile of 16S rRNA and 18S rRNA gene and real-time PCR assay. In addition, a 7-day lab incubation under constantly 25°C was conducted to further track the changes in metabolic activity. While the decrease under metal pollution in MBC and MBN, as well as in culturable population size, total PLFA contents and DGGE band numbers of bacteria were not significantly and consistently seen, a significant reduction was indeed observed under metal pollution in microbial quotient, in culturable fungal population size and in ratio of fungal to bacterial PLFAs consistently across the sites by an extent ranging from 6% to 74%. Moreover, a consistently significant increase in metabolic quotient was observed by up to 68% under pollution across the sites. These observations supported a shift of microbial community with decline in its abundance, decrease in fungal proportion and thus in C utilization efficiency under pollution in the soils. In addition, ratios of microbial quotient, of fungal to bacterial and qCO₂ are proved better indicative of heavy metal impacts on microbial community structure and activity. The potential effects of these changes on C cycling and CO₂ production in the polluted rice paddies deserve further field studies.

Assessment and modification of degenerate qPCR primers that amplify functional genes from etheneotrophs and vinyl chloride-assimilators

AIMS

Degenerate qPCR primer sets that target the functional genes etnC and etnE in etheneotrophs and vinyl chloride-assimilating bacteria were assessed and modified in an effort to improve performance.

METHODS AND RESULTS

Functional gene abundance in four pure cultures was estimated by qPCR using novel (MRTC and MRTE) and existing (RTC and RTE) degenerate primer sets and compared to abundances estimated with nondegenerate gene-specific primers (GSPs). Functional gene abundance in groundwater DNA extracted from several contaminated sites was also estimated with MRTC and MRTE primers.

CONCLUSIONS

MRTC primers displayed significantly improved etnC quantification in both pure cultures and environmental samples.

SIGNIFICANCE AND IMPACT OF THE STUDY

Application of MRTC and MRTE primer sets will enhance microbial ecology studies involving etheneotrophs and qPCR analyses that support vinyl chloride bioremediation strategies.

Dynamics of bacterial communities during solid-state fermentation using agro-industrial wastes to produce poly-γ-glutamic acid, revealed by real-time PCR and denaturing gradient gel electrophoresis (DGGE)

The dynamics of bacterial communities play an important role in solid-state fermentation (SSF). Poly-γ-glutamic acid (γ-PGA) was produced by Bacillus amyloliquefaciens C1 in SSF using dairy manure compost and monosodium glutamate production residuals as basic substrates. The production of γ-PGA reached a maximum of 0.6% after 20 days fermentation. Real-time polymerase chain reaction showed the amount of total bacteria reached 3.95 × 10(9) 16S rDNA copies/g sample after 30 days, which was in good accordance with the 4.80 × 10(9) CFU/g obtained by plate counting. Denaturing gradient gel electrophoresis profile showed a reduction of microbial diversity during fermentation, while the inoculum, B. amyloliquefaciens C1, was detected as the dominant organism through the whole process. In the mesophilic phase of SSF, Proteobacteria was the dominant microbial, which was replaced by Firmicutes and Actinobacteria in the thermophilic phase. The molecular analysis of the bacterial diversity has significant potential for instructing the maturing process of SSF to produce γ-PGA at a large-scale level, which could be a benefit in the production of high quality and stable SSF products.

Nested PCR bias: a case study of Pseudomonas spp. in soil microcosms

Nested PCR methods combined with denaturing gradient gel electrophoresis (DGGE) are widely used for the detection of low copy number species or for the analysis of group-specific community profiles. With an appropriate number of PCR cycles during the first round of amplification, initial differences in the copy numbers of different DNA fragments that are targeted can be maintained during the second round without significant bias. However, if an excessive number of cycles in used in the first round, relative differences in the copy numbers of the targeted sequences can be obscured. Here we demonstrate the effect of "nested PCR bias" in a case study with PCR-DGGE of 16S rRNA gene sequences targeting Pseudomonas spp. following exposure of soil to naphthalene vapors. Our results demonstrate artifacts caused by nested PCR bias can be substantially minimized by calibrating the number of first round PCR cycles, thereby preserving the ability to obtain semiquantitative data for evaluating changes in gene copy numbers over time.