Denaturing Gradient Gel Electrophoresis Fingerprinting Research Articles

Yeast diversity in pit mud and related volatile compounds in fermented grains of chinese strong-flavour liquor

Chinese strong-flavour liquor is produced via a traditional solid-state fermentation strategy facilitated by live microorganisms in pit mud-based cellars. For the present analysis, pit mud samples from different spatial locations within fermentation cellars were collected, and the yeast communities therein were assessed via culture-based and denaturing gradient gel electrophoresis (DGGE) approaches. These analyses revealed significant differences in the composition of yeast communities present in different layers of pit mud. In total, 29 different yeast species were detected, and principal component analyses revealed clear differences in microbial diversity in pit mud samples taken from different cellar locations. Culture-dependent strategies similarly detected 20 different yeast species in these samples. However, while Geotrichum silvicola, Torulaspora delbrueckii, Hanseniaspora uvarum, Saturnispora silvae, Issatchenkia orientalis, Candida mucifera, Kazachstania barnettii, Cyberlindnera jadinii, Hanseniaspora spp., Alternaria tenuissima, Cryptococcus laurentii, Metschnikowia spp., and Rhodotorula dairenensis were detected via a PCR-DGGE approach, they were not detectable in culture-dependent analyses. In contrast, culture-based approaches led to the identification of Schizosaccharomyces pombe and Debaryomyces hansenii in these pit mud samples, whereas they were not detected using DGGE fingerprints profiles. An additional HS-SPME-GC-MS-based analysis of the volatile compounds present in fermented grains samples led to the identification of 66 such compounds, with the highest levels of volatile acids, esters, and alcohols being detected in fermented grains from lower layer samples. A canonical correspondence analysis (CCA) suggested they were significant correlations between pit mud yeast communities and associated volatile compounds in fermented grains.

Cooperation among phosphate-solubilizing bacteria, humic acids and arbuscular mycorrhizal fungi induces soil microbiome shifts and enhances plant nutrient uptake

BackgroundIncreasing the presence of beneficial soil microorganisms is a promising sustainable alternative to support conventional and organic fertilization and may help to improve crop health and productivity. If the application of single bioeffectors has shown satisfactory results, further improvements may arise by combining multiple beneficial soil microorganisms with natural bioactive molecules.MethodsIn the present work, we investigated in a pot experiment under greenhouse conditions whether inoculation of two phosphate-solubilizing bacteria, Pseudomonas spp. (B2) and Bacillus amyloliquefaciens (B3), alone or in combination with a humic acids (HA) extracted from green compost and/or a commercial inoculum (M) of arbuscular mycorrhizal fungi (AMF), may affect maize growth and soil microbial community. Phospholipid fatty acid (PLFA) and denaturing gradient gel electrophoresis (DGGE) fingerprinting analysis were performed to detect changes in the microbial community composition.ResultsPlant growth, N and P uptake, and mycorrhizal root colonization were found to be larger in all inoculated treatments than in the uninoculated control. The greatest P uptake was found when B. amyloliquefaciens was applied in combination with both HA and arbuscular mycorrhizal fungi (B3HAM), and when Pseudomonas was combined with HA (B2HA). The PLFA-based community profile revealed that inoculation changed the microbial community composition. Gram+/Gram− bacteria, AMF/saprotrophic fungi and bacteria/fungi ratios increased in all inoculated treatments. The greatest values for the AMF PLFA marker (C16:1ω5) and AMF/saprotrophic fungi ratio were found for the B3HAM treatment. Permutation test based on DGGE data confirmed a similar trend, with most significant variations in both bacterial and fungal community structures induced by inoculation of B2 or B3 in combination with HA and M, especially in B3HAM.ConclusionsThe two community-based datasets indicated changes in the soil microbiome of maize induced by inoculation of B2 or B3 alone or when combined with humic acids and mycorrhizal inoculum, leading to positive effects on plant growth and improved nutrient uptake. Our study implies that appropriate and innovative agricultural management, enhancing the potential contribution of beneficial soil microorganisms as AMF, may result in an improved nutrient use efficiency in plants.

Dietary tryptophan depletion alters the faecal bacterial community structure of compulsive drinker rats in schedule-induced polydipsia

RationaleCompulsive behaviour, present in different psychiatric disorders such as obsessive-compulsive disorder, schizophrenia and drug abuse, is associated with altered levels of serotonin (5-hydroxytryptamine, 5-HT). The gut microbiota regulates tryptophan (TRP) metabolism and may affect global 5-H synthesis in the enteric and central nervous systems, suggesting a possible involvement of gut microbiota in compulsive spectrum disorders. ObjectivesThe present study investigated whether chronic TRP depletion by diet alters the faecal bacterial community profiles of compulsive versus non-compulsive rats in schedule-induced polydipsia (SIP). Peripheral plasma 5-HT and brain-derived neurotrophic factor (BDNF) levels were evaluated. MethodsWistar rats were selected as High Drinkers (HD) or Low Drinkers (LD) according to their SIP behaviour and were fed for 14 days with either a TRP-free diet (T-) or a TRP-supplemented diet (T+). The faecal bacterial community structure was investigated with 16S rRNA gene-targeted denaturing gradient gel electrophoresis (DGGE) fingerprinting analysis. ResultsCompulsive HD rats showed a lower bacterial diversity than LD rats, irrespectively of the diet. The TRP-depleted HD rats, the only group increasing compulsive licking in SIP, showed a reduction of bacterial evenness and a highly functionally organized community compared with the other groups, indicating that this bacterial community is more fragile to external changes due to the dominance of a low number of species. The chronic TRP depletion by diet effectively reduced peripheral plasma 5-HT levels in both HD and LD rats, while plasma BDNF levels were not altered. ConclusionsThese results highlight the possible implication of reduced microbial diversity in compulsive behaviour and the involvement of the serotonergic system in modulating the gut brain-axis in compulsive spectrum disorders.

The Dynamics Analysis of Fungal Community Diversity During the Fermentation Process of Chinese Traditional Soybean Paste

The aim of this work was to monitor the microflora and the changing principle of the fungi family at the natural fermented soybean paste different fermentation stage. It obtained the V4 and V5 regions of the 18S rDNA by extracting the fungal genomic DNA from the natural fermented soybean paste. DGGE fingerprint of fungal 18S rDNA V4 (partial), V5 sections during the different soybean paste fermentation periods of 17 samples were line analyzed. The abundance, the absorbance and the degree of dominance and diversity indexes of fungal community were determined by the denaturing gradient gel electrophoresis (DGGE). The V4, V5 regions of 18S rDNA of the complex microbial community in the fermentation of traditional soybean paste were around 762 bp and 422 bp, and there were 9 kinds of microorganisms discovered, which were Penicillium expansum, Aspergillus oryzae, Mucor, P. commune, Absidia corymbifera, M. racemosus, Actinomucor elegans, Aspergillus, and an unculturable fungi. The DGGE ecological analysis showed that the unculturable fungi and A. oryzae were dominant microorganisms all the time, and the highest diversion index of 2.87 was reached at 56 days of fermentation. This study laid a foundation for researching suitable soybean paste artificial inoculation and also provided a good help for the fermentation process of soybean paste.

Traceability of different brands of bottled mineral water during shelf life, using PCR-DGGE and next generation sequencing techniques

Natural mineral waters contain indigenous bacteria characteristic of each spring source. Once bottled, these communities change over time until the water is consumed. Bottle material is believed to play a major role in the succession of these populations, but very few studies to date have evaluated the effect of this material on bacterial communities. In this study, we examined the microbial community structure of three natural mineral waters over 3 months after bottling in glass and polyethylene terephthalate (PET) bottles. To this end, we used culture-dependent (heterotrophic plate count) and culture-independent methods (16S rRNA massive gene sequencing, denaturing gradient gel electrophoresis (DGGE) and fluorescent microscopy with vital dyes). Total and viable cell counts increased by around 1–2 log10 units between 1 and 2 weeks after bottling and then remained constant over 3 months for all waters regardless of the bottle material. DGGE fingerprints and 16S rRNA massive sequencing analysis both indicated that different communities were established in the waters two weeks after bottling in the different bottle materials. In conclusion, no differences in total, viable and culturable bacteria counts were observed between mineral waters bottled with PET or glass during shelf life storage. Nevertheless, in spite of changes in the communities, each water brand and material presented a distinct microbial community structure clearly distinguishable from the others, which could be interesting for traceability purposes.

Plant-microbe interactions endorse growth by uplifting microbial community structure of Bacopa monnieri rhizosphere under nematode stress

The modification of rhizosphere microbial diversity and ecological processes are of rising interest as shifting in microbial community structure impacts the mutual role of host–microbe interactions. Nevertheless, the connection between host-microbial community diversity, their function under biotic stress in addition to their impact on plant performances is poorly understood. The study was designed with the aim to analyze the tripartite interactions among Chitiniphilus sp., Streptomyces sp. and their combination with indigenous rhizospheric microbial population of Bacopa monnieri for enhancing the plant growth and bacoside A content under Meloidogyne incognita stress. Overall, plants treated with the microbial combination recorded enhanced growth as illustrated by significantly higher biomass (2.0 fold), nitrogen uptake (1.8 fold) and bacoside A content (1.3 fold) along with biocontrol efficacy (58.5%) under nematode infected field. The denaturing gradient gel electrophoresis (DGGE) fingerprints of 16S-rDNA revealed that microbial inoculations are major initiators of bacterial community structure in the plant rhizosphere. Additionally, the plants treated with microbial combination showed maximum diversity viz., Shannon’s (3.29), Margalef’s (4.21), and Simpson’s (0.96) indices. Likewise the metabolic profiling data also showed a significant variation among the diversity and evenness indices upon microbial application on the native microflora. We surmise that the application of beneficial microbes in combinational mode not only helped in improving the microbial community structure but also successfully enhanced plant and soil health under biotic stress.

Effects of microplastics on trophic parameters, abundance and metabolic activities of seawater and fish gut bacteria in mesocosm conditions.

Plastic pollution is an emerging threat with severe implications on animals' and environmental health. Nevertheless, interactions of plastic particles with both microbial structure and metabolism are a new research challenge that needs to be elucidated yet. To improve knowledge on the effects played by microplastics on free-living and fish gut-associated microbial community in aquatic environments, a 90-day study was performed in three replicated mesocosms (control-CTRL, native polyvinyl chloride-MPV and weathered polyvinyl chloride-MPI), where sea bass specimens were hosted. In CTRL mesocosm, fish was fed with no-plastic-added food, whilst in MPV and MPI food was supplemented with native or exposed to polluted waters polyvinylchloride pellets, respectively. Particulate organic carbon (POC) and nitrogen, total and culturable bacteria, extracellular enzymatic activities, and microbial community substrate utilization profiles were analyzed. POC values were lower in MPI than MPV and CRTL mesocosms. Microplastics did not affect severely bacterial metabolism, although enzymatic activities decreased and microbes utilized a lower number of carbon substrates in MPI than MPV and CTRL. No shifts in the bacterial community composition of fish gut microflora were observed by denaturing gradient gel electrophoresis fingerprinting analysis.

Prevalence of antibiotic-resistant coliform bacteria, Enterococcus spp. and Staphylococcus spp. in wastewater sewerage biofilm.

Urban wastewater contains various micropollutants and a high number of different micro-organisms. Some bacteria in wastewater can attach to surfaces and form biofilm, which gives bacteria an advantage in the fight against environmental stresses. This work focused on analysis of bacterial communities in biofilms isolated from influent and effluent sewerage of a wastewater treatment plant (WWTP) in Bratislava, Slovakia. Detection of biofilm microbiota was performed by culture-independent and -dependent approaches. The composition of bacterial strains was detected by denaturing gradient gel electrophoresis fingerprinting coupled with construction of 16S rRNA clone libraries. Analysis of the concentration of antibiotics and the prevalence of antibiotic-resistant coliforms, Enterococcus spp. and Staphylococcus spp. in sewerage was also studied. Biofilm collected at the inlet point was characterised primarily by the presence of Pseudomonas spp., Acinetobacter spp. and Janthinobacterium spp. clones, whilst members of the genus Pseudomonas were largely detected in biofilm isolated in outflow of the WWTP. Predominant antibiotics such as azithromycin, clarithromycin and ciprofloxacin were found in influent wastewater. The removal efficiency of these antibiotics, notably azithromycin and clarithromycin, was 30% in most cases. The highest number of antibiotic-resistant bacteria, with a predominance of coliforms, was detected in samples of effluent biofilm. Multidrug-resistant strains in effluent biofilm showed very good biofilm-forming ability.

Effector gene vap1 based DGGE fingerprinting to assess variation within and among Heterodera schachtii populations.

Abstract Populations of beet cyst nematodes Heterodera schachtii vary in aggressiveness and virulence toward sugar beet varieties, but also in traits like host range, or decline rate in the field. Diversity of their essential pathogenicity gene vap1 is shaped by diversifying selection and gene flow. The authors developed a technique to study inter-population variation and intra-population diversity and dynamics of H. schachtii based on the gene vap1. Degenerate primers were designed to amplify, clone, and sequence this gene from diverse species and populations of cyst nematodes. This resulted in a high diversity of sequences for H. schachtii, and allowed to design non-degenerated primers to amplify a fragment suitable for sequence dependent separation of gene variants in denaturing gradient gel electrophoresis (DGGE). The developed primers span a highly variable intron and part of a slightly variable exon. A marker comprised of the 14 mostly detected gene variants was established for gel-to-gel comparisons. For individual juveniles up to six gene variants were resolved and substantial variation within and among cysts was observed. A fast and easy DNA extraction procedure for 20 pooled cysts was established, which provided DGGE patterns with high similarity among replicate samples from field populations. Permutation tests on pairwise similarities within and among populations showed significant differences among vap1 patterns of field populations of H. schachtii. Similarly, gene diversity as expressed by the Shannon index was statistically different among field populations. In conclusion, the DGGE technique is a fast and – compared to sequencing approaches – inexpensive tool to compare populations of H. schachtii and link observed biological characteristics to genetic pattern.

Microalgae community shifts during the biogas upgrading in an alkaline open photobioreactor.

To achieve the functional specialization of a microalgae community through operational tuning of an open photobioreactor used for biogas upgrading under alkaline conditions. An open photobioreactor was inoculated with an indigenous microalgae sample from the Texcoco Soda Lake. A microalgae community was adapted to fix CO2 from synthetic biogas through different culture conditions reaching a maximum of 220mg CO2 l-1 per day. Picochlorum sp. and Scenedesmus sp. were identified as the prominent microalgae genera by molecular fingerprinting (partial sequencing of 16S rRNA and 18S rRNA genes) but only the first was detected by microscopy screening. Changes in the microalgae community profile were monitored by a range-weighted richness index, reaching the lowest value when biogas was upgraded. A robust microalgae community in the open photobioreactor was obtained after different culture conditions. The specialization of microalgae community for CO2 fixation under H2 S presence was driven by biogas upgrading conditions. The alkaline conditions enhance the CO2 absorption from biogas and could optimize specialized microalgae communities in the open photobioreactor. Denaturing gradient gel electrophoresis fingerprinting and richness index comparison are useful methods for the evaluation of microalgae community shifts and photosynthetic activity performance, particularly in systems intended for CO2 removal from biogas where the CO2 assimilation potential can be related to the microbial richness.

Microbial community structure and activity in trace element-contaminated soils phytomanaged by Gentle Remediation Options (GRO)

Gentle remediation options (GRO) are based on the combined use of plants, associated microorganisms and soil amendments, which can potentially restore soil functions and quality. We studied the effects of three GRO (aided-phytostabilisation, in situ stabilisation and phytoexclusion, and aided-phytoextraction) on the soil microbial biomass and respiration, the activities of hydrolase enzymes involved in the biogeochemical cycles of C, N, P, and S, and bacterial community structure of trace element contaminated soils (TECS) from six field trials across Europe. Community structure was studied using denaturing gradient gel electrophoresis (DGGE) fingerprinting of Bacteria, α- and β-Proteobacteria, Actinobacteria and Streptomycetaceae, and sequencing of DGGE bands characteristic of specific treatments. The number of copies of genes involved in ammonia oxidation and denitrification were determined by qPCR.Phytomanagement increased soil microbial biomass at three sites and respiration at the Biogeco site (France). Enzyme activities were consistently higher in treated soils compared to untreated soils at the Biogeco site. At this site, microbial biomass increased from 696 to 2352 mg ATP kg−1 soil, respiration increased from 7.4 to 40.1 mg C-CO2 kg−1 soil d−1, and enzyme activities were 2–11-fold higher in treated soils compared to untreated soil. Phytomanagement induced shifts in the bacterial community structure at both, the total community and functional group levels, and generally increased the number of copies of genes involved in the N cycle (nirK, nirS, nosZ, and amoA). The influence of the main soil physico-chemical properties and trace element availability were assessed and eventual site-specific effects elucidated. Overall, our results demonstrate that phytomanagement of TECS influences soil biological activity in the long term.

Relationships between and formation dynamics of the microbiota of consumers, producers, and the environment in an abalone aquatic system.

An ecosystem is a community comprising living and nonliving components of the environment. Microbes are ubiquitous elements in each of these components. The dynamics of microbiota formation in an ecosystem is important to elucidate, because how the different components of a system exchange microbes, and how the microbes control ecological processes remain unresolved. In this study, an abalone, Haliotis diversicolor, seed-nursing pond was used as a model system. We first examined changes in bacterial communities during the seedling cultivation of this herbivorous juvenile aquatic invertebrate animal. Denaturing gradient gel electrophoresis (DGGE) and pyrosequencing were used to analyze bacterial community dynamics and spatio-temporal interactions of different system components: consumers (abalone), producers (algae or a substrate), and the environment (water). DGGE fingerprints revealed that the developmental stages of abalone influences bacterial communities of both the abalone and substrate. Although the communities in water fluctuated daily, they could be divided into two clusters that coincided with abalone stages, reflecting the transition from larva to juvenile at around day 21. Pyrosequencing showed that the microbiota in the abalone and substrate had more operational taxonomic units in common than that of either with water. The Bray-Curtis similarity index was used to quantify the formation dynamics of microbiota among the various components of the system. The bacterial communities in producers and consumers showed similar changes. These communities were unstable at the beginning and then slowly stabilized over time. The environmental bacterial community was more stable than the bacterial communities in consumers and producers, and may have been the basis for stability in the system. Our research provides insights into the dynamics of microbiota formation in various biotic elements of a system that will contribute to predictive systems modeling.

Study on community structure of microbial consortium for the degradation of viscose fiber wastewater

BackgroundEnrichment culture was applied to obtain microbial consortium from activated sludge samples collected from biodegradation system, a chemical fiber plant in Hebei Province, China. Bacterial composition and community dynamic variation were assessed employing denaturing gradient gel electrophoresis fingerprinting technology based on amplified 16S rRNA genes in the entire process of enrichment culture for viscose fiber wastewater.ResultsFour bacteria named as VF01, VF02, VF03, and VF04 were isolated from the microbial consortium adopting the spray-plate method. The DNA bands of these four bacteria were corresponded to the predominant DNA bands in the electrophoresis pattern. VF01, VF02, VF03, and VF04 were phylogenetically closed to Bacillus licheniformis, Bacillus subtilis, Paracoccus tibetensis, and Pseudomonas sp. by sequence analysis, respectively. The degradation effects for CODCr of single isolated strain, mixed strains, and microbial consortium (VF) originally screened from viscose fiber wastewater were determined. The degradation ability was as follows: microbial consortium (VF) > mixed strains > single isolated strain. Microbial consortium (VF) showed the optimum degradation rate of CODCr of 87% on 14th day. Degradation of pollutants sped up by bio-augmentation of four strains. The molecular weight distribution of organic matter showed that viscose fiber wastewater contained a certain amount of large molecular organic matter, which could be decomposed into smaller molecular substances by microbial consortium (VF).ConclusionsThe microbial consortium (VF) obtained from enrichment culture exhibited great potential for CODCr degradation. The screened strains had bio-augmentation functions and the addition of a mixture of four bacteria could speed up the degradation rate of pollutants.

Microbial investigations in throat swab and tracheal aspirate specimens are beneficial to predict the corresponding endotracheal tube biofilm flora among intubated neonates with ventilator-associated pneumonia.

Ventilator-associated pneumonia (VAP) is a common nosocomial infection in neonatal intensive care units with high morbidity and mortality. Bacterial biofilm in the endotracheal tube (ET) provides a notable and persistent source of pathogens that may cause VAP, and thus is important for VAP detection. However, during intubation microbial investigations in ET, samples are unavailable due to the infeasibility of collecting ET samples during intubation of neonates. It is therefore of great importance to find alternative sources of samples that can help identify the ET biofilm flora. In the present study, the microbial signatures of throat swabs and tracheal aspirates were compared with ET biofilm samples from VAP neonates using 16S ribosomal RNA gene polymerase chain reaction, denaturing gradient gel electrophoresis (DGGE), cloning and sequencing. Sequences were assigned to phylogenetic species using BLAST. Microbial diversity and richness among the three types of specimens were compared based on their DGGE fingerprints, and taxonomic characteristics based on the BLAST results. The microbial richness and diversity of ET biofilms were similar to tracheal aspirate yet significantly different from throat swab samples (P<0.05). Compared with ET biofilms, the overall constituent ratio of microflora was significantly different in throat swab and tracheal aspirate samples (P<0.05). However tracheal aspirate samples were useful for predicting Staphylococcus sp. in ET biofilms with a sensitivity of 85.7% and a specificity of 83.3%. The sensitivity for the combination of tracheal aspirate and throat swab samples to detect Staphylococcus sp. in ET biofilms was 100%. The detection of Pseudomonas sp. in throat swabs assisted its identification in ET biofilms (sensitivity 33.3% and specificity 100%). The results of the present study suggest that microbial investigations in throat swab and tracheal aspirate samples are beneficial for identifying the ET biofilm flora. There may therefore be clinical applications of using substituent samples to identify pathogens in ET biofilms for VAP surveillance among intubated neonates.

Denaturing gradient gel electrophoresis profiles of bacteria from the saliva of twenty four different individuals form clusters that showed no relationship to the yeasts present

ObjectivesThe aim was to investigate the relationship between groups of bacteria identified by cluster analysis of the DGGE fingerprints and the amounts and diversity of yeast present. MethodsBacterial and yeast populations in saliva samples from 24 adults were analysed using denaturing gradient gel electrophoresis (DGGE) of the bacteria present and by yeast culture. ResultsEubacterial DGGE banding patterns showed considerable variation between individuals. Seventy one different amplicon bands were detected, the band number per saliva sample ranged from 21 to 39 (mean±SD=29.3±4.9). Cluster and principal component analysis of the bacterial DGGE patterns yielded three major clusters containing 20 of the samples. Seventeen of the 24 (71%) saliva samples were yeast positive with concentrations up to 103cfu/mL. Candida albicans was the predominant species in saliva samples although six other yeast species, including Candida dubliniensis, Candida tropicalis, Candida krusei, Candida guilliermondii, Candida rugosa and Saccharomyces cerevisiae, were identified. The presence, concentration, and species of yeast in samples showed no clear relationship to the bacterial clusters. ConclusionDespite indications of in vitro bacteria-yeast interactions, there was a lack of association between the presence, identity and diversity of yeasts and the bacterial DGGE fingerprint clusters in saliva. This suggests significant ecological individual-specificity of these associations in highly complex in vivo oral biofilm systems under normal oral conditions.

Evaluation of different PCR primers for denaturing gradient gel electrophoresis (DGGE) analysis of fungal community structure in traditional fermentation starters used for Hong Qu glutinous rice wine

Denaturing gradient gel electrophoresis (DGGE) has become a widely used tool to examine microbial community structure. However, when DGGE is applied to evaluate the fungal community of traditional fermentation starters, the choice of hypervariable ribosomal RNA gene regions is still controversial. In the current study, several previously published fungal PCR primer sets were compared and evaluated using PCR-DGGE, with the purpose of screening a suitable primer set to study the fungal community of traditional fermentation starters for Hong Qu glutinous rice wine.Firstly, different primer sets were used to amplify different hypervariable regions from pure fungal cultures. Except NS1/FR1+ and ITS1fGC/ITS4, other primer sets (NL1+/LS2R, NL3A/NL4GC, FF390/FR1+, NS1/GCFung, NS3+/YM951r and ITS1fGC/ITS2r) amplified the target DNA sequences successfully. Secondly, the selected primer sets were further evaluated based on their resolution to distinguish different fungal cultures through DGGE fingerprints. Three primer sets (NL1+/LS2R, NS1/GCFung and ITS1fGC/ITS2r) were finally selected for investigating the fungal community structure of different traditional fermentation starters for Hong Qu glutinous rice wine. The internal transcribed spacer (ITS) region amplified by ITS1fGC/ITS2r, which is more hypervariable than the 18S rRNA gene and 26S rRNA gene, provides an excellent tool to separate amplification products of different fungal species. Results indicated that PCR-DGGE profile using ITS1fGC/ITS2r showed more abundant fungal species than that using NL1+/LS2R and NS1/GCFung. Therefore, ITS1fGC/ITS2r is the most suitable primer set for PCR-DGGE analysis of fungal community structure in traditional fermentation starters for Hong Qu glutinous rice wine. DGGE profiles based on ITS1fGC/ITS2r revealed the presence of twenty-four fungal species in traditional fermentation starter. A significant difference of fungal community can be observed directly from DGGE fingerprints and principal component analysis. The statistical analysis results based on the band intensities of fungal DGGE profile showed that Saccharomyces cerevisiae, Saccharomycopsis fibuligera, Rhizopus oryzae, Monascus purpureus and Aspergillus niger were the dominant fungal species.In conclusion, the comparison of several primer sets for fungal PCR-DGGE would be useful to enrich our knowledge of the fungal community structures associated with traditional fermentation starters, which may facilitate the development of better starter cultures for manufacturing Chinese Hong Qu glutinous rice wine.

Symbiodinium (Dinophyceae) community patterns in invertebrate hosts from inshore marginal reefs of the southern Great Barrier Reef, Australia.

The broad range in physiological variation displayed by Symbiodinium spp. has proven imperative during periods of environmental change and contribute to the survival of their coral host. Characterizing how host and Symbiodinium community assemblages differ across environmentally distinct habitats provides useful information to predict how corals will respond to major environmental change. Despite the extensive characterizations of Symbiodinium diversity found amongst reef cnidarians on the Great Barrier Reef (GBR) substantial biogeographic gaps exist, especially across inshore habitats. Here, we investigate Symbiodinium community patterns in invertebrates from inshore and mid-shelf reefs on the southern GBR, Australia. Dominant Symbiodinium types were characterized using denaturing gradient gel electrophoresis fingerprinting and sequencing of the ITS2 region of the ribosomal DNA. Twenty one genetically distinct Symbiodinium types including four novel types were identified from 321 reef-invertebrate samples comprising three sub-generic clades (A, C, and D). A range of host genera harbored C22a, which is normally rare or absent from inshore or low latitude reefs in the GBR. Multivariate analysis showed that host identity and sea surface temperature best explained the variation in symbiont communities across sites. Patterns of changes in Symbiodinium community assemblage over small geographic distances (100s of kilometers or less) indicate the likelihood that shifts in Symbiodinium distributions and associated host populations, may occur in response to future climate change impacting the GBR.

Effects on soil quality of biochar and straw amendment in conjunction with chemical fertilizers

The objective of this study was to evaluate the effects on chemical and microbiological properties of paddy soil of short-term biochar, straw, and chemical fertilizers compared with chemical fertilization alone. Five soil fertilization treatments were evaluated: regular chemical fertilizers (RF), straw+regular chemical fertilizers (SRF), straw biochar+regular chemical fertilizers (SCRF), bamboo biochar (BC)+regular chemical fertilizers (BCRF), and straw biochar+70% regular chemical fertilizers (SC+70%RF). Their effects were investigated after approximately 1.5 years. The soil pH and cation exchange capacity (CEC) were significantly higher in biochar-treated soils. The soil phosphorous (P) and potassium (K) contents increased with biochar application. The soil Colwell P content was significantly increased with the addition of straw biochar in the treatments of SCRF and SC+70%RF. The oxygen (0):carbon (C) ratio doubled in BC picked from the soil. This indicated that BC underwent a significant oxidation process in the soil. The denaturing gradient gel electrophoresis (DGGE) fingerprints of microbial communities differed among the treatments. Soils with added biochar had higher Shannon diversity and species richness indices than soils without biochars. The results suggest that biochar can improve soil fertility.

Dynamic changes of yak (Bos grunniens) gut microbiota during growth revealed by polymerase chain reaction-denaturing gradient gel electrophoresis and metagenomics.

ObjectiveTo understand the dynamic structure, function, and influence on nutrient metabolism in hosts, it was crucial to assess the genetic potential of gut microbial community in yaks of different ages.MethodsThe denaturing gradient gel electrophoresis (DGGE) profiles and Illumina-based metagenomic sequencing on colon contents of 15 semi-domestic yaks were investigated. Unweighted pairwise grouping method with mathematical averages (UPGMA) clustering and principal component analysis (PCA) were used to analyze the DGGE fingerprint. The Illumina sequences were assembled, predicted to genes and functionally annotated, and then classified by querying protein sequences of the genes against the Kyoto encyclopedia of genes and genomes (KEGG) database.ResultsMetagenomic sequencing showed that more than 85% of ribosomal RNA (rRNA) gene sequences belonged to the phylum Firmicutes and Bacteroidetes, indicating that the family Ruminococcaceae (46.5%), Rikenellaceae (11.3%), Lachnospiraceae (10.0%), and Bacteroidaceae (6.3%) were dominant gut microbes. Over 50% of non-rRNA gene sequences represented the metabolic pathways of amino acids (14.4%), proteins (12.3%), sugars (11.9%), nucleotides (6.8%), lipids (1.7%), xenobiotics (1.4%), coenzymes, and vitamins (3.6%). Gene functional classification showed that most of enzyme-coding genes were related to cellulose digestion and amino acids metabolic pathways.ConclusionYaks’ age had a substantial effect on gut microbial composition. Comparative metagenomics of gut microbiota in 0.5-, 1.5-, and 2.5-year-old yaks revealed that the abundance of the class Clostridia, Bacteroidia, and Lentisphaeria, as well as the phylum Firmicutes, Bacteroidetes, Lentisphaerae, Tenericutes, and Cyanobacteria, varied more greatly during yaks’ growth, especially in young animals (0.5 and 1.5 years old). Gut microbes, including Bacteroides, Clostridium, and Lentisphaeria, make a contribution to the energy metabolism and synthesis of amino acid, which are essential to the normal growth of yaks.

Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) Profile of Bacterial Community from Agricultural Soils in Bauchi, North-East Nigeria

The population dynamics of bacterial community was investigated in three Agricultural soils, designated as Loamy sand (A), Peaty coarse (B) and Loamy coarse sand (C) in North-East, Nigeria. The soil chemical properties were characterized to fully understand their nature. Metagenomic approach was used to extract soil DNA using the fast DNA Spin Kit extraction technique. The PCR-electrophoresed DNA bands were excised and subjected to a full scale Denaturing Gradient Gel Electrophoresis (DGGE) analysis. DGGE fingerprinting for the PCR-16S rDNA product revealed a diverse profile of complex population of bacterial community in the study area. The study shows that more bacterial community can be fully investigated using molecular techniques rather than traditional culture method. The implication of the results obtained is discussed.