Reaction-denaturing Gradient Gel Electrophoresis Research Articles

The role of TiO2 and gC3N4 bimetallic catalysts in boosting antibiotic resistance gene removal through photocatalyst assisted peroxone process

Antibiotics are extensively used in human medicine, aquaculture, and animal husbandry, leading to the release of antimicrobial resistance into the environment. This contributes to the rapid spread of antibiotic-resistant genes (ARGs), posing a significant threat to human health and aquatic ecosystems. Conventional wastewater treatment methods often fail to eliminate ARGs, prompting the adoption of advanced oxidation processes (AOPs) to address this growing risk. The study investigates the efficacy of visible light-driven photocatalytic systems utilizing two catalyst types (TiO2-Pd/Cu and g-C3N4-Pd/Cu), with a particular emphasis on their effectiveness in eliminating blaTEM, ermB, qnrS, tetM. intl1, 16 S rDNA and 23 S rDNA through photocatalytic ozonation and peroxone processes. Incorporating O3 into photocatalytic processes significantly enhances target removal efficiency, with the photocatalyst-assisted peroxone process emerging as the most effective AOP. The reemergence of targeted contaminants following treatment highlights the pivotal importance of AOPs and the meticulous selection of catalysts in ensuring sustained treatment efficacy. Furthermore, Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) analysis reveals challenges in eradicating GC-rich bacteria with TiO2 and g-C3N4 processes, while slight differences in Cu/Pd loadings suggest g-C3N4-based ozonation improved antibacterial effectiveness. Terminal Restriction Fragment Length Polymorphism analysis highlights the efficacy of the photocatalyst-assisted peroxone process in treating diverse samples.

Impact of whole grain highland hull-less barley on the denaturing gradient gel electrophoresis profiles of gut microbial communities in rats fed high-fat diets.

While next-generation sequencing has overshadowed polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), the latter still holds promise for advancing gut microbiota analysis due to its unique advantages. In this study, we used optimized nested PCR-DGGE to investigate the gut microbiota profile of high-fat diet rats after administering whole grain highland hull-less barley. High-throughput sequencing was employed to validate the DGGE results. Our results proved the reliability of PCR-DGGE for analyzing the dominant taxonomic composition while also providing visual evidence of a notable relationship between the composition of cecal and fecal microbial communities, highlighting substantial differences in both richness and abundance.

Symbiont Diversity in Imidacloprid-Resistant and Imidacloprid-Susceptible Populations of Nilaparvata lugens (Hemiptera: Delphacidae)1

Abstract Imidacloprid, a neonicotinoid insecticide, is efficacious against hemipterans, including the brown planthopper, Nilaparvata lugens (Stål) (Hemiptera: Delphacidae). However, frequent use of this insecticide has resulted in the development of high levels of resistance among brown planthopper populations. Endosymbionts of insects have contributed to host physiology and evolution and play a role in resistance to chemical toxins. In this study, polymerase chain reaction–denaturing gradient gel electrophoresis was used to analyze the bacterial and yeast-like symbiont communities of imidacloprid-resistant and -susceptible brown planthopper populations. The Shannon-Weaver diversity index and the evenness index indicated no differences in the richness and the expression of overall species distribution of the symbiotic communities of resistant and susceptible populations. The similarity coefficients of 0.53 and 0.56 for bacterial and yeast-like symbionts, respectively, indicated the main types of differences among microorganisms in resistant and susceptible populations. Sequence comparison analysis indicated the bacterial species in the susceptible population were members of the Enterobacteriaceae and Moraxellaceae, and those in the resistant population were members of the Enterobacteriaceae, Oxalobacteriaceae, Rhodobacteriaceae, and Sphingomonadaceae. Differences also were found in the composition of yeast-like symbionts of the two populations; Cryptococcus luteolus, Pseudozyma aphidis, and Pseudozyma antarctica were detected in the susceptible population, and Cladosporium perangustum was detected in the resistant population.

Occurrence of sulfate-reducing bacteria in well water: identification of anaerobic sulfidogenic bacterial enrichment cultures.

Bacteriological studies of well water mainly focus on aerobic and facultative aerobic coliform bacteria. However, the presence of obligate anaerobic bacteria in well water, especially sulfate-reducing bacteria (SRB), possible causative agents of some diseases, is often ignored. In this study, the presence of SRB and coexisting anaerobic bacteria with SRB in sulfate-reducing enrichment cultures obtained from 10 well water samples in Istanbul was investigated. A nested polymerase chain reaction-denaturing gradient gel electrophoresis strategy was performed to characterize the bacterial community structure of the enrichments. The most probable number method was used to determine SRB number. Out of 10, SRB growth was observed in only one (10%) enrichment culture and the SRB number was low (<10 cells/mL). Community members were identified as Desulfolutivibrio sulfodismutans and Anaerosinus sp. The results show that SRB coexist with Anaerosinus sp., and this may indicate poor water quality, posing a risk to public health. Furthermore, Anaerosinus sp., found in the human intestinal tract, may be used as an alternative anaerobic fecal indicator. It is worth noting that the detection of bacteria using molecular analyzes following enrichment culture techniques can bring new perspectives to determine the possible origin and presence of alternative microbial indicators in aquatic environments.

Agronomic strategies to enhance the early vigor and yield of maize. Part I: the role of seed applied biostimulant, hybrid and starter fertilization on rhizosphere bacteria profile and diversity.

The sustainable intensification of maize-based systems may reduce greenhouse-gas emissions and the excessive use of non-renewable inputs. Considering the key role that the microbiological fertility has on crop growth and resilience, it is worth of interest studying the role of cropping system on the rhizosphere bacterial communities, that affect soil health and biological soil fertility. In this work we monitored and characterized the diversity and composition of native rhizosphere bacterial communities during the early growth phases of two maize genotypes of different early vigor, using a nitrogen (N)-phosphorus (P) starter fertilization and a biostimulant seed treatment, in a growth chamber experiment, by polymerase chain reaction-denaturing gradient gel electrophoresis of partial 16S rRNA gene and amplicon sequencing. Cluster analyses showed that the biostimulant treatment affected the rhizosphere bacterial microbiota of the ordinary hybrid more than that of the early vigor, both at plant emergence and at the 5-leaf stage. Moreover, the diversity indices calculated from the community profiles, revealed significant effects of NP fertilization on richness and the estimated effective number of species (H2) in both maize genotypes, while the biostimulant had a positive effect on plant growth promoting community of the ordinary hybrid, both at the plant emergence and at the fifth leaf stage. Our data showed that maize genotype was the major factor shaping rhizosphere bacterial community composition suggesting that the root system of the two maize hybrids recruited a different microbiota. Moreover, for the first time, we identified at the species and genus level the predominant native bacteria associated with two maize hybrids differing for vigor. These results pave the way for further studies to be performed on the effects of cropping system and specific crop practices, considering also the application of biostimulants, on beneficial rhizosphere microorganisms.

A Novel: Low-cost Method for the Isolation of Anaerobic Hydrogen Producing Bacteria

The hydrogen content of the two sludge samples namely TDS and PLS were increased after the heat shock pretreatment from 239.23 ± 10.23 mL/L to 663.87 ± 15.99 mL/L at 80°C and from 173.61 ± 17.21 mL/L to 496.74 ± 30.21 mL/L at 60°C, respectively. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) indicated that Enterococcus and Clostridium were the dominant bacteria in the TDS and PLS consortium. Two strains were successfully isolated from TDS and PLS using a simple method. Based on Bergey’s key identification and 16S rDNA sequencing, they were identified as Clostridium butyricum strain TD and Clostridium acetobutylicum strain PL. The hydrogen content, glucose consumed yield, and hydrogen yield of C. butyricum TD and C. acetobutylicum PL were 545.24 ± 7.31 mL/L, 90 ± 0.41 %, 0.89 ± 0.01 mol H2/mol glucose, and 729.34 ± 22.81 mL/L, 92.77 ± 1.39 %, 1.26 ± 0.05 mol H2/mol glucose, respectively.

Effects of p-Hydroxyphenylacetic Acid and p-Hydroxybenzoic Acid on Soil Bacterial and Fungal Communities

Soil phenolic acids mainly come from crop residue and root exudates, which are often reported as allelochemicals affecting crop growth and soil microbial community. Here, two phenolic acid compounds, p-hydroxyphenylacetic acid (HPA) and p-hydroxybenzoic acid (HBA) were amended to the soils and were incubated under room conditions, and the soil samples were collected from soybean and corn fields separately. The soil microbial community was determined by PCR-DGGE (polymerase chain reaction-denatured gradient gel electrophoresis) and clone methods. Microbial biomass carbon (MBC) was measured based on the fumigation–extraction method. The result revealed that HPA/HBA amendment significantly affected soil bacterial and fungal community structures. HPA/HBA enriched some distinct bacteria and fungi. The induced bacteria were mainly Gemmatimonas, Bacillus, and Acidobacteria, while the induced fungi were mainly Penicillium and Aspergillus. HPA amendment enhanced the more bacterial quantities of corn and soybean soils than HBA. The fungal diversity in corn and soybean soils treated with HBA was higher than that treated with HPA. It was speculated that the diversity of degrading HBA fungi was higher than that of degrading HPA. This study comprehensively analyzed the effects of phenolic acids on soil microbial community and increased the understanding of the monoculture barrier to agricultural production.

Bacterial and fungal community composition and community-level physiological profiles in forest soils.

We characterized the potential functioning and composition of the bacterial and fungal communities in the O and A horizons of forest soils using community-level physiological profile (CLPP) based on BIOLOG analysis, and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis of 16S and 18S rDNA fragments, respectively. In addition, relationships between the potential functioning and the community composition in each horizon, and between the O and A horizons, were assessed using Procrustes analysis. For the bacterial and fungal communities, the CLPP and DGGE profile were clearly separated between the O and A horizons in a principal coordinate analysis except for the fungal CLPP. No significant links for CLPP and DGGE profile between the O and A horizons were observed for either bacterial or fungal communities, suggesting that different factors had considerable influence on the microbial communities between the O and A horizons. Significant couplings between bacterial and fungal DGGE profiles (p <0.05 for O horizon; p <0.01 for A horizon), and between bacterial and fungal CLPPs (p = 0.001 for O horizon; p <0.01 for A horizon), were observed in the O and A horizons, implying that common factors strongly influenced the bacterial and fungal communities in each horizon. Although a significant correlation was observed between bacterial community composition and the potential functioning in the A horizon (p <0.01), such a correlation was not observed for the fungal community in the A horizon, and for the bacterial and fungal communities in the O horizon. This finding suggested that potential functioning, which would reflect only rapidly growing microorganisms, was not strongly associated with the composition of the entire microbial community. Further studies are needed to unravel the factors shaping the composition and functioning of microbial communities in forest soils.

Removal of Hydrogen Sulfide from Swine-Waste Biogas on a Pilot Scale Using Immobilized Paracoccus versutus CM1.

Hydrogen sulfide (H2S) is a toxic and corrosive component that commonly occurs in biogas. In this study, H2S removal from swine-waste biogas using sulfur-oxidizing Paracoccus versutus CM1 immobilized in porous glass (PG) and polyurethane foam (PUF) biofilters was investigated. Bacterial compositions in the biofilters were also determined using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). The biofilters were first tested on a laboratory scale under three space velocities (SV): 20, 30, and 40 h-1. Within 24 h, at an SV of 20 h-1, PG and PUF biofilters immobilized with P. versutus CM1 removed 99.5% and 99.7% of H2S, respectively, corresponding to the elimination capacities (EC) of 83.5 and 86.2 gm-3 h-1. On a pilot scale, with the horizontal PG-P. versutus CM1 biofilter operated at an SV of 30 h-1, a removal efficiency of 99.7% and a maximum EC of 113.7 gm-3 h-1 were achieved. No reduction in methane content in the outlet biogas was observed under these conditions. The PCR-DGGE analysis revealed that Paracoccus,&amp;nbsp;Acidithiobacillus, and Thiomonas were the predominant bacterial genera in the biofilters, which might play important roles in H2S removal. This PG-P. versutus CM1 biofiltration system is highly efficient for H2S removal from swine-waste biogas.

Q-PCR Methodology for Monitoring the Thermophilic Hydrogen Producers Enriched from Elephant Dung

This study aims to create a quantitative polymerase chain reaction (q-PCR) methodology for monitoring the hydrogen-producing mixed cultures enriched from elephant dung using alpha-cellulose as a carbon source through five generations of repetitive sub-culture. The enriched thermophilic mixed cultures from the fifth cultivation cycle gave the highest hydrogen yield of 170.3 mL H2/g cellulose and were used to generate hydrogen from sawdust. Clostridium sp. and Thermoanaerobacterium sp. were the dominant bacteria in thermophilic mixed cultures with high hydrogen yield, according to polymerase chain reaction-denatured gradient gel electrophoresis (PCR-DGGE). q-PCR primers Chis150F and ClostIR, TherF and TherR, and BacdF and BacdR were developed to amplify the 16S rRNA genes of Clostridium sp., Thermoanaerobacterium sp., and Bacillus sp., respectively, for the quantification of hydrogen-producing bacteria in biohydrogen fermentation. Similar q-PCR analysis of Clostridium sp., Thermoanaerobacterium sp., and Bacillus sp. 16S rRNA gene amplification during hydrogen production from cellulose and sawdust revealed increasing gene copy number with time. The molecular approaches developed in this study can be used to monitor microbial communities in hydrogen fermentation processes efficiently.

Roughage biodegradation by natural co-cultures of rumen fungi and methanogens from Qinghai yaks

Anaerobic fungus–methanogen co-cultures from rumen liquids and faeces can degrade lignocellulose efficiently. In this study, 31 fungus–methanogen co-cultures were first obtained from the rumen of yaks grazing in Qinghai Province, China, using the Hungate roll-tube technique. The fungi were identified according to morphological characteristics and internal transcribed spacer (ITS) sequences. The methanogens associated with each fungus were identified by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and 16S rRNA gene sequencing. They were five co-culture types: Neocallimastix frontalis + Methanobrevibacter ruminantium, Neocallimastix frontalis + Methanobrevibacter gottschalkii, Orpinomyces joyonii + Methanobrevibacter ruminantium, Caecomyces communis + Methanobrevibacter ruminantium, and Caecomyces communis + Methanobrevibacter millerae. Among the 31 co-cultures, during the 5-day incubation, the N. frontalis + M. gottschalkii co-culture YakQH5 degraded 59.0%–68.1% of the dry matter (DM) and 49.5%–59.7% of the neutral detergent fiber (NDF) of wheat straw, corn stalk, rice straw, oat straw and sorghum straw to produce CH4 (3.0–4.6 mmol/g DM) and acetate (7.3–8.6 mmol/g DM) as end-products. Ferulic acid (FA) released at 4.8 mg/g DM on corn stalk and p-coumaric acid (PCA) released at 11.7 mg/g DM on sorghum straw showed the highest values, with the following peak values of enzyme activities: xylanase at 12,910 mU/mL on wheat straw, ferulic acid esterase (FAE) at 10.5 mU/mL on corn stalk, and p-coumaric acid esterase (CAE) at 20.5 mU/mL on sorghum straw. The N. frontalis + M. gottschalkii co-culture YakQH5 from Qinghai yaks represents a new efficient combination for lignocellulose biodegradation, performing better than previously reported fungus–methanogen co-cultures from the digestive tract of ruminants.

Mapping Archaeal Diversity in Soda Lakes by Coupling 16S rRNA PCR-DGGE Analysis with Remote Sensing and GIS Technology

The haloarchaeal diversity of four hypersaline alkaline lakes from the Wadi El-Natrun depression (Northern Egypt) was investigated using culture-independent polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) of 16S rRNA gene phylotypes, which was combined with remote sensing and geographic information system (GIS) data to highlight the distribution pattern of the microbial diversity in water and sediment samples. The majority of archaeal sequences identified in all four lakes belonged to the phyla Euryarchaeota and Crenarchaeota. Sediment samples from Beida Lake and water samples from El-Hamra Lake showed the highest levels of archaeal diversity. Sequence similarities ≥ 95% were found between six of the acquired clones and uncultured Halorhabdus, Euryarchaeota, and archaeon clones. In addition, two clones shared a high level of sequence similarity (97%) with unclassified archaea, while other nine clones exhibited 96% to 99% sequence similarity with uncultured archaeon clones, and only one clone showed 97% identity with an uncultured Crenarchaeota. Likewise, 7 DGGE bands presented a sequence similarity of 90 to 98% to Halogranum sp., Halalkalicoccus tibetensis, Halalkalicoccus jeotgali, uncultured Halorubrum, Halobacteriaceae sp., or uncultured haloarchaeon. In conclusion, while the variety of alkaliphilic haloarchaea in the examined soda lakes was restricted, the possibility of uncovering novel species for biotechnological applications from these extreme habitats remains promising.

Simultaneous removal of ammonia nitrogen and sulfide by coupled anammox and sulfur autotrophic denitrification process from industrial wastewater

This work presents an experimental study on the coupling between anammox and sulfur autotrophic denitrification for simultaneous removal of ammonia nitrogen and sulfide in industrial wastewater, leading to less environmental pollution. In a low-load continuous operation mode hybrid anaerobic baffled reactor (HABR) was started with 7 <pH<8.2 and temperature 30–35 °C. After 60 d of continuous operation successful enrichment of methanogenic granular sludge (MGS) size 7 and 5 mm was achieved. In the mature granular sludge phase (HRT 10 h), with influent chemical oxygen demand (COD) 1100 mg/L, the effluent COD 90 mg/L and removal efficiency was 90%. The MLSS, MLVSS, and f values were 9520, 6980, and 0.7. After 42 d of continuous operation with influent COD 600–700 mg/L, NO3−-N 250-300 mg/L, and COD/NO3−-N 2 to 2.8 (temperature 30–35 °C and pH 6.5–7.5) successful enrichment of denitrifying granular sludge (DGS) was achieved. In the research, the anammox start-up periods in MGS and DGS reactors are 86 and 118 d. An experimental comparative analysis to explore the influence of COD/TN 1:1,1:1.8,1:4.5, and 1:8.5 on the two reactors was performed. For COD/TN 1:1.8, the NH4+-N, NO2−-N, and TN removal efficiency were 54%, 73%, and 52%. The removal efficiency of the #2 reactors NH4+-N, NO2−-N, and TN were 50%, 60%, and 55%. S2−/NO3−-N of 2:5, 3.5:5, 5:5, 6.5:5 were investigated. Influent pH 7.5–8.0, temperature 30–35 °C and HRT 6.5 h, with average influent NH4+-N, NO3−-N, S2−, COD concentration 60, 25, 75, and 25 mg/L, the maximum removal efficiency of #1 reactor was 70%, 97%, 82%, and 100%. For 2# reactor 82%, 99%, 84%, and 100%. When MGS as carrier, the NH4+-N, NO3−-N, and S2− removal efficiency reached 67.67%, 98.59%, and 99.1%. With DGS as carrier, the NH4+-N, NO3−-N, and S2− removal efficiency reached 81.82%, 98.69%, and 84.18%. However, the coupling phase S0 production and productivity results showed that the DGS reactor was significantly better than the MGS reactor. Under the same hydraulic conditions the two reactors successfully coupled after 54 d of operation. Additionally, polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) analysis, revealed that the microbial community change is related to the concentration of organic matter, nitrogen and sulfur in the water. Building on these findings, future study will focus on the optimization of the mix design to provide practical engineering guidance.

Effects of Chlorothalonil Application on the Physio-Biochemical Properties and Microbial Community of a Yellow–Brown Loam Soil

To gain better knowledge of the effects of residual chlorothalonil on soil characteristics and soil microbial communities, we evaluated the dissipation of chlorothalonil and the effects of different chlorothalonil concentrations on soil respiration, enzyme activities, and microbial community structure in yellow–brown loam soils. Bacterial and fungal soil communities were examined using traditional plate counting and polymerase chain reaction–denaturing gradient gel electrophoresis (PCR–DGGE) methods. Soil properties and the results of DGGE band analysis were both used to estimate the status of the soil microbial ecosystem. The results show that residual chlorothalonil has considerable effects on soil respiration, enzymatic activities, and microbial community structure. In particular, soil respiration and phosphatase activities were increased, while saccharase activity, microbial biomass, and microbial community diversity were decreased by increasing levels of chlorothalonil treatment. Correlation analyses revealed that the application of chlorothalonil was significantly correlated with the change of the soil respiration, urease activity, sucrase activity, soil culturable bacteria, and culturable fungi biomass. We conclude that residual chlorothalonil is directly related to soil respiration, enzyme activities, and microbial community structure.

Sex Difference of Effect of Sophora flavescens on Gut Microbiota in Rats.

Objective By observing the sex difference of the gut microbiota in rats and the influence of Sophora flavescens (S. flavescens) on the gut microbiota in rats of different genders, it is hoped that it can provide reference materials for the rational use of S. flavescens in clinical practice. Method Taking samples of the jejunum (containing intestinal contents) and feces of 8-week-old rats, and detecting the composition of gut microbiota of females and males by 16S rRNA sequencing technology; At the same time, 8-week-old rats were gavaged with different doses of S. flavescens decoction, and the duodenum, jejunum, ileum, and colon (including the intestinal contents) samples were collected at 1, 2, and 3 weeks, using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) technology and real-time fluorescent quantitative PCR (qRT-PCR) technology to observe the changes in the structure and the quantitative changes of 4 major intestinal dominant bacteria Enterococcus, Bacteriodes, Lactobacillus, and Clostridium in each intestinal segment, respectively. Result (1) The gut microbiota of normal rats without administration also had obvious gender differences; (2) S. flavescens significantly affects the composition of gut microbiota, and in different intestinal segments, this effect was different between genders under different dosages and different continuous administration times. Conclusion The effect of S. flavescens on the gut microbiota of rats had gender differences.

Effect of diets containing full-fat Hermetia illucens on rainbow trout microbiota: A dual cultivation-independent approach with DGGE and NGS

Given the drift to improve economic and ecological sustainability of the aquaculture sector, novel ingredients fulfilling these requirements are sought. Hermetia illucens, commonly called black soldier fly, (Diptera: Stratiomydae; H) is a promising dietary protein source but its effect on fish gut microbiota is still to be clarified. The aim of the present study was to increase the knowledge of the effect of dietary full-fat H meal on rainbow trout (Oncorhynchus mykiss) microbiota and, in particular, on intestinal mucosa-adherent microbiota by applying a dual approach based on polymerase chain reaction-denaturing gradient gel electrophoresis and high-throughput sequencing of the 16S rRNA gene. Rainbow trout (initial body weight of 137.3 ± 10.5 g) was fed for 98 days with a control diet (H0) containing fishmeal and protein-rich vegetable ingredients and an experimental diet (H50) where 50% of the fishmeal had been replaced by full-fat H meal rich in saturated fatty acids.Proteobacteria, Firmicutes and Actinobacteria were generally present in all samples, although the core microbiota (relative prevalence higher than or equal to 80% in all samples) only consisted of the proteobacteria Caulobacter, Delftia, Agrobacterium and Ochrobactrum. In addition, Streptococcus infantis and a member of the Cytophagaceae family were part of the core taxa of mucosa samples. Tenericutes were abundant in pyloric caeca samples and, among them, Mycoplasmataceae seemed to increase in the group fed the high saturated fatty acid diet containing H meal; a consideration about the connection between this bacterial group and the dietary lipid content must be considered. Dietary treatment did not clearly affect alpha-diversity metrics, but mucosa samples tended to be more resilient to dietary changes than content samples. Permutational analysis of variance showed significantly different β-diversities between diets (p < 0.05) but principal coordinates analysis did not confirm this result.Diets for rainbow trout containing full-fat H meal determined interesting modifications in the gut microbiota with patterns similar to the ones found in the literature. The dietary lipids can exert an effect on microbiota. Nonetheless, research data on this topic are still scarce and further studies are highly encouraged.

Evidence of functional and structural changes in the microbial community beneath a succulent invasive plant in coastal dunes

Abstract Coastal dunes represent priority habitats for conservation due to the provision of valuable ecosystem services such as land protection, water supply or biodiversity conservation. Soil microbial communities are of crucial importance to maintain plant diversity due to harsh environmental conditions, water limitation and nutrient scarcity. Invasive alien plants represent a major threat to ecosystem conservation. Here, we explored different impacts of Carpobrotus edulis, a succulent plant invading coastal areas worldwide, on the function and structure of bacterial communities. Sand represents a challenging substrate due to low organic matter content and limited microbial activity. We optimized bacterial extraction for functional evaluation before assessing ecosystem impacts produced by C. edulis. We compared 12 extracting procedures combining different soil storage, sample amount and extracting solutions on the functional activity of sand communities through the community-level physiological profile. We further explored the function (using Biolog Ecoplates) and structure [using polymerase chain reaction–denaturing gradient gel electrophoresis (PCR-DGGE)] of bacterial communities from dunes invaded by C. edulis. Saline solution consistently increased bacterial cells detected by cytometry (P ≤ 0.001). Principal component analysis suggested a limited temporal framework (0–24 h) in which community function can be explored without significant alterations in C substrate consumption. Changes under C. edulis invasion exhibited a different pattern of C substrate utilization comparing native and non-native zones (interspecific), but also between native zones (intraspecific), suggesting that functional impacts are site-dependent. Complementary, results obtained from PCR-DGGE indicated that the bacterial community structure of native dunes significantly differed from dunes invaded by C. edulis.

A comparison of nitrogen removal efficiencies and microbial communities between anammox and de-ammonification processes in lab-scale ASBR, and full-scale MBBR and IFAS plants

Anammox and deammonification processes under different five-day biochemical oxygen demand (BOD5) to total nitrogen (TN) ratios (0, 0.1, and 0.2) were investigated in a lab-scale anaerobic sequencing batch reactor (ASBR) and full-scale moving bed bioreactor (MBBR) and integrated fixed-film activated sludge (IFAS) systems operated under different conditions (dissolved oxygen (DO) concentrations, solids retention time (SRTs), organic and ammonia-nitrogen (NH3-N) loading rates). Nitrogen removal efficiencies for the lab-scale ASBR anammox process using synthetic wastewater as substrate and two full-scale deammonification processes (MBBR with anaerobic digester centrate as substrate and IFAS with stored landfill leachate as substrate) were >90%, ∼60%, and ∼75%, respectively. Quantitative polymerase chain reaction and polymerase chain reaction-denaturing gradient gel electrophoresis were used to investigate microbial communities on three different attached-growth media: scrub sponges (ASBR), AnoxKaldnes K5 (MBBR) and polypropylene (IFAS). The anammox species, Candidatus Brocadia fulgida was dominant only in the lab-scale anammox system and Candidatus Kuenenia sp. was dominant under DO concentration of 0.3 mg l−1 and organic loading of 0.04 kg-BOD·m−3·d−1. Candidatus Jettenia caeni was dominant at BOD5:TN ratio of 0.2 and organic loading up to 0.39 kg-BOD·m−3·d−1 and NH3-N loading 1.95 kg-N·m−3·d−1. Furthermore, abundance of amoA-AOA populations in lab-scale and two full-scales treatment systems were similar (around 8.04 × 104 to 1.56 × 105 copies/g-sludge) but different predominant AOA species were observed on the different media. Based on the results from this work, maintaining low BOD5:TN ratios could be applied to improve the nitrogen removal efficiency of deammonification processes. While very low BOD5:TN ratio was the primary determinant of deammonification efficiency, other beneficial influences include high specific surface area carriers, low DO concentration, high temperature, and long SRT.

PCR-DGGE Analysis Proves the Suppression of Rhizoctonia and Sclerotium Root Rot Due to Successive Inoculations

The soil-borne pathogens Rhizoctonia solani and Sclerotium rolfsii have emerged as major pathogens of radish (Raphanus sativus) worldwide. The induction of soil suppressive of radish root rot disease was evaluated in soil repeatedly inoculated with R. solani, nonpathogenic binucleate Rhizoctonia sp. AG-A W1 (BNR) and S. rolfsii. The repeated inoculations of soil with R. solani and BNR significantly suppressed the disease severity of R. solani and S. rolfsii compared to the control. In contrast, the repeated inoculation of soil with S. rolfsii significantly suppressed only the pathogen, S. rolfsii. The community structure was examined using PCR-DGGE (polymerase chain reaction denaturing gradient gel electrophoresis) method. The bands of Trichoderma sp. were observed in the first, second and third inoculations of the soil with BNR. Similarly, bands of Trichoderma sp. were observed in the second and third inoculations of the soil with S. rolfsii and R. solani. Compared to the control, disease severity was significantly reduced in the soil repeatedly inoculated with S. rolfsii and R. solani . In conclusion, Trichoderma species were accumulated in specific patterns depending on the applied fungal inoculum in the suppressive soil.

Analysis of rice microbial communities under different storage conditions using culture-dependent and -independent techniques

Rice is a staple food for over half of the world’s population, and fungal spoilage in stored rice may occur when the moisture content and temperature are conducive. Aspergillus sp. and Penicillium sp. are the most harmful toxigenic species that produce harmful mycotoxins. Molds pose a potential threat to public health and cause a huge economic loss. Therefore, it is of great importance to find out how molds multiply in rice. This study focused on the isolation and identification of fungi presented in rice and their evolution in rice with different moisture contents stored for varying periods of time and under different temperatures. Mold community was detected every month using the culture-dependent and -independent method of polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Significant differences were detected by the traditional culture method under different storage conditions. For potato dextrose agar (PDA) media, high temperature and moisture were suitable for the dominant strains including Penicillium aurantiogriseum and Penicillium oxalicum. In particular, P. oxalicum competitively inhibited the other fungi. For Rose Bengal medium, no difference was observed under different storage conditions, and only typical strains such as Aspergillus candidus and Alternaria were detected. PCR-DGGE identified some uncultured strains such as Trichoderma sp. and Cladosporium sp., the dominant strains and the flora diversity such as Aspergillus restrictus and Eurotium athecium. These results indicated that storage conditions greatly shape fungal growth. This study provides a foundation for the evolution of fungal flora in rice during storage in China and may help in developing biological control methods to prevent mold contamination in rice.