Denaturing Gradient Gel Electrophoresis Bands Research Articles

Response of Bacterial Community Structure in the Bulk Soil and Rice Straw Residues under Different Crop Rotation Systems

This study investigated the effect of upland crop rotation on soil bacterial community in bulk soil and rice straw residues in the alluvial soils. Soil samples and rice straw residues in two crop rotation models including triple rice and rice-upland crops were collected for incubation under anaerobic and aerobic conditions. Data were analyzed from Denaturing Gradient Gel Electrophoresis band patterns. The results showed that the composition and diversity of communities colonizing the rice straw residues differed from those inhabiting the bulk soil. The bacterial community composition and diversity were only moderately affected by rice straw residues in the bulk soil. Especially, this study indicated that the composition of the bacterial community associated with the bulk soil and rice straw residues was dynamic in two incubation conditions (aerobic or anaerobic) and the different crop rotation models. The findings of this study demonstrated that the bacterial diversity was not affected by the difference in continuous paddy rice cultivation compared to the upland crop rotation system.

Biosurfactant-Producing Bacteria and Microbial Analysis in Mae Soon Reservoir, Fang Oil Field, Chiang Mai, Thailand

Microbial Enhanced Oil Recovery (MEOR) is an effective alternative method for oil recovery in reservoirs using microorganisms or their secondary metabolites. This research aimed to evaluate the indigenous bacteria from Mae Soon reservoir by culture-dependent and culture-independent methods and to investigate the potential of biosurfactant-producing bacteria using a drop-collapsed assay. Indigenous bacteria were isolated from the oil sands of the reserved core of Mae Soon reservoir using fi ve different media (nutrient, Luria-Bertani, mineral salt, tryptic soy, and peptone yeast extract). Fifty-four facultative anaerobic bacterial isolates were obtained. Seven isolates showed their potential as biosurfactant producers in the drop-collapse assay. Based on 16S rRNA gene analysis, six of the biosurfactant-producing bacterial isolates belonged to the species Bacillus licheniformis and one belonged to the species B. subtilis. The biosurfactant producers and microbial community in the oil sands were determined using Denaturing Gradient Gel Electrophoresis (DGGE). Interestingly, DGGE bands corresponding to bacteria belonging to the genus Geobacillus sp. were detected. Overall, the results obtained from this work showed that indigenous bacteria in Mae Soon reservoir oil well were prospective for use in MEOR.

Seasonal variations in cyanophage communities in the coastal waters of Kuwait

Cyanobacteria and the viruses that infect them (cyanophages) are crucial to the marine ecosystem, but little is known regarding the genetic diversity of natural cyanophages and their variation over space and time in Kuwait waters. In this study, we explored the seasonal diversity of cyanophages specifically the cyanomyophages in the coastal waters of Kuwait using denaturing gradient gel electrophoresis (DGGE) and cloning sequencing by targeting the portal protein-encoding gene g20. Surface- and deep-water samples were collected bimonthly from three coastal sites over a period of 14 months.The DGGE bands for both the surface- and deep-water samples revealed a dramatic seasonal variation in cyanomyophages across all sites but with no spatial variations. The bands exhibited a similar pattern in the warmer season (June to October), with very intense bands observed specifically for the samples collected in August and October compared to those collected in winter-spring (January to April). Furthermore, g20 clone libraries prepared from single-month samples provided evidence of depth-related differences in cyanomyophage communities. Phylogenetic analysis indicated that the most abundant g20 operational taxonomic units (OTUs) clustered with the ubiquitous culture-containing cyanomyophage marine cluster II. In addition, the obtained OTUs were closely related to cyanophages infecting Synechococcus and Prochlorococcus hosts. This study demonstrated the seasonal diversity of cyanophages in the coastal waters of Kuwait, and the diversity appeared to be greater in deep water. This highlights the need for further studies to determine whether these temporal changes in cyanophage community abundance and diversity reflect recurring annual patterns.

Storage time and temperature affect microbial dynamics of yeasts and acetic acid bacteria in a kombucha beverage

Kombucha is a mildly sweet, slightly acidic fermented beverage, commercially available worldwide, that has attracted increasing consumers' interest due to its potential health benefits. Kombucha is commonly prepared using sugared black or green tea, but also other plant substrates are frequently utilised. Kombucha is obtained by fermentation using a symbiotic culture of bacteria and yeasts, whose composition varies depending on inoculum origin, plant substrates and environmental conditions. After fermentation, kombucha drinks are usually refrigerated at 4 °C, in order to maintain their biological and functional properties. There are no reports on the fate of microbial communities of kombucha in relation to long-term storage time and temperature. Here, for the first time, we monitored the diversity and dynamics of the microbial communities of a kombucha beverage fermented with different herbs during storage at 4 °C and at room temperature, for a period of 90 days, utilising culture-dependent and independent approaches. Moreover, cultivable yeasts and acetic acid bacteria (AAB) were isolated from the beverage, inoculated in pure culture, identified by molecular methods, and yeasts assessed for their functional properties. Total yeast counts were not affected by storage temperature and time, although their community composition changed, as Saccharomyces species significantly decreased after 45 days of storage at room temperature, completely disappearing after 90 days. On the other hand, Dekkera anomala (Brettanomyces anomalus), representing 52 % of the yeast isolates, remained viable up to 90 days at both storage temperatures, and was able to produce high levels of organic acids and exopolysaccharides. Data from DGGE (Denaturing Gradient Gel Electrophoresis) band sequencing confirmed that it was the dominant yeast species in all samples across storage. Other yeast isolates were represented by Saccharomyces and Zygosaccharomyces species. Among AAB, Gluconobacter oxydans, Novacetimonas hansenii and Komagataeibacter saccharivorans represented 46, 36 and 18 % of the isolates, whose occurrence remained unchanged across storage at 4 °C and did not vary up to 20 days of storage at room temperature. This work showed that the combination of culture-dependent and independent approaches is important for obtaining a complete picture of the distinctive core microbial community in kombucha beverages during storage, elucidating its diversity and composition, and preliminary characterizing yeast strains with putative functional activities.

Effect of Jhum Cycles on <i>Acidobacteria</i> and <i>Burkholderia</i> Community in the Rhizosphere of Mixed Crops of Different Jhum Fields

In the present study, culture-dependent and independent [Denaturing gradient gel electrophoresis (DGGE)] approach were used to analyze the effect of fallow cycle on bacterial populations associated with mixed crops selected from three different jhum fallow cycles (5-, 10- and 20- years) of Changki village, Nagaland. Two important bacterial phyla viz. Acidobacteria and Burkholderia were selected for DGGE analysis. According to the DGGE banding profile, Acidobacteria showed more richness compared Burkholderia. The presence and absence of few of the bands in the profile indicate the community shifts in the selected jhum fields. Shannon diversity index was higher in Acidobacteria than Burkholderia. Multivariate analysis showed that Acidobacteria community structure was similar among the crop plants of the same fallow cycle. Burkholderia community did not show clear separation among fallow cycles although crop of same fallow cycle tend to group together. ANOSIM and PERMANOVA showed significant differences in rhizosphere community pattern among fallow cycles and the crop plants of same fallow cycles indicated that both fallow cycle and crop plants are factors determining the Acidobacteria and Burkholderia community composition in jhum soils which was also confirmed by the culture-dependent analysis. Culturable bacterial counts were dependent on media used and significantly different at different fallow cycles. Bacterial communities (both culturable and DGGE patterns) were correlated with soil nutrients suggesting their importance in stability of jhum soil. The present study revealed that both fallow cycle and host plant may be the key factors in shaping many bacterial communities in jhum soils.

Susceptibility and resilience of the soil ciliate community to high temperatures

ABSTRACT Ciliates play important ecological roles as microbial predators in soil. Although arable soils can experience a wide range of temperatures caused by agricultural land management, the effect of temperature on soil ciliates has been poorly documented, particularly for high temperatures over 30°C. Here, we studied the response of the soil ciliate community to different temperatures in comparison with that of the bacterial and fungal communities. Soils collected from a greenhouse were supplemented with organic fertilizer and incubated at different temperatures (10–60°C). Ciliate trophozoites were detected in the pore water of the soils incubated at 20°C and 10°C, while no trophozoites were observed at temperatures of 30°C and higher. The diversity of the ciliate community represented by fingerprints of denaturing gradient gel electrophoresis (DGGE) also decreased at temperatures higher than 20°C. A few DGGE bands were exclusively dominated at 40°C. The ciliate community composition in the soil incubated at 40°C recovered after subsequent incubation at 20°C, suggesting the resilience of the ciliate community to heat stress. Such recovery was not observed in the soil incubated at 60°C, probably because of the lethal effect on most soil ciliates. The responses of the ciliate community to temperature were similar to those of the fungal community, while the bacterial community showed higher resistance and resilience than the ciliate and fungal communities. The results suggested that temperature is an important factor controlling the ciliate community and affects the structure and functions of the soil microbial food web.

Long-term effect of non-irrigation and irrigation on soil Pythium, Fusarium, and Rhizoctonia communities and their relation with seed-rot, root-rot, and damping-off of soybean

Long-term non-irrigation (N-IRR) and irrigation (IRR) might affect pathogen communities causing seed-rot, root-rot, and damping-off of soybean. Characterization and quantification of Pythium, Fusarium, and Rhizoctonia spp. are critical for understanding the ecology of these microorganisms and management of root diseases. The populations and communities of Pythium, Fusarium, and Rhizoctonia were assessed in soils with long-term N-IRR and IRR using soil dilution plating, denaturing gradient gel electrophoresis (DGGE), and DNA sequence analysis. Disease incidences of seed-rot, root-rot, and damping-off of soybean were also evaluated with the soils from N-IRR and IRR in a growth chamber. Results showed that the population densities of Pythium and Rhizoctonia based on dilution plating and richness based on DGGE were significantly lower in soils with N-IRR than IRR, whereas the population densities of Fusarium and richness of Fusarium were significantly higher in soils with N-IRR than IRR. Cluster analysis based on DGGE band patterns demonstrated that the communities of Pythium, Fusarium, and Rhizoctonia were separated based on N-IRR and IRR. Species diversities of some Pythium, Fusarium, or Rhizoctonia were impacted differently in soils with N-IRR and IRR. Moreover, canonical correspondence analysis (CCA) showed that the disease incidences were positively correlated with levels of soil moisture, pH, the populations of Pythium and Rhizoctonia, richness of Pythium and Rhizoctonia, and negatively correlated with soil porosity, humic matter, and potassium. Long-term N-IRR and IRR could impact pathogen populations and communities and disease incidences differently, and the disease complex might be caused by different species under different systems.

Effect of Tidal Cycles on Bacterial Biofilm Formation and Biocorrosion of Stainless Steel AISI 316L

The effects of tidal cycles associated with the water level on the biocorrosion of stainless steel AISI 316L were studied. Steel coupons were exposed to different conditions of immersion in mesocosms fed by fresh seawater either continuously or in accordance with the periodicity of natural tides. After 5 and 15 weeks, all coupons were found to have undergone ennoblement associated with the formation of a biofilm. Analysis of the composition of the bacterial community using denaturing gradient gel electrophoresis (DGGE) revealed differences in the biological succession. After 15 weeks, exposure to the simulated tidal conditions resulted in biofilms with lesser bacterial richness; the corresponding rate of corrosion, as determined by weight loss, was about 40 times lower compared to the case for the continuous exposure to seawater. Phylogenetic analysis of selected DGGE bands and the inspection of biofilm morphologies revealed that the faster rate of corrosion was associated with the presence of iron-oxidizing Zetaproteobacteria and eukaryotic photosynthetic microorganisms. On the other hand, intermittent exposure to seawater resulted in the succession of microorganisms resistant to the stress associated with sudden environmental changes, which was associated with a low rate of corrosion.

Metagenomic Analysis of Bacteria Phylum Firmicutes and Bacteroidetes in Women with Type 2 Diabetes

Diabetes mellitus (DM) is a serious health problem in Indonesia. Type 2 diabetes is a metabolic disease which primarily caused by obesity-linked insulin resistance. There is a link between insulin resistance and bacterial populations in the gut. Therefore, the aims of this study was to analyze composition of bacteria belong to the phylum Firmicutes and Bacteroidetes in women with type 2 diabetes and non-diabetic persons as control. The study included five female adults type 2 diabetes patients and five healthy controls. The bacteria composition was analyzed for abundance by denaturing gradient gel electrophoresis (DGGE). Metagenomic analysis based on 16S rRNA gene was represented by 12 DGGE bands. The twelve respective bands showed the similarity ranging from 77 up to 98%. Diversity of microbial composition in women type 2 diabetes was represented by five DGGE bands are Bacteroides fragilis, Bacteroides vulgatus, uncultured Bacteroides sp. clone Lb4eF4, uncultured bacterium clone 16sms90-5g05, and uncultured bacterium clone Malaga 1F14. Four DGGE bands in women healthy controls are closely related to uncultured bacterium isolate DGGE gel band Eub42, uncultured bacterium isolate DGGE gel band K115, uncultured bacterium clone HFV04255, and Enterococcus sp. the finding shows bacterial species belong to the phylum Bacteroidetes was mostly found in women diabetic group, while those belong to the phylum Firmicutes was mostly found in healthy controls.

Bifidobacterias como indicadoras de contaminación fecal en aguas tropicales

Human fecal pollution in water constitute a serious risk to the public health, nevertheless the indicator microorganisms commonly used to detect the levels of fecal pollution does not identify the specific source. The detection of certain Bifidobacterium species as B. adolescentis and B. dentium have been proposed as an effective marker of human fecal contamination, but this has not yet been demonstrated in tropical environmental conditions. The aim of the present work was to determine the Bifidobacteria profile in one sample of water from the Mesolandia Swamp in the Colombian Caribbean and feces samples of 260 human and 94 domestic animals from a human settlement around the swamp. DNA from all the samples was amplified by PCR using specific specie primers based on the 16S rRNA gene sequence and separated by DGGE (Denaturing Gradient Gel Electrophoresis). DGGE bands were excised, reamplified, sequenced, and compared to GenBank database. Bifidobacterial DGGE profiles showed that eight species of Bifidobacterium that were found in the water sample, were also present in the human and animal feces. Bifidobacterium adolescentis and B. dentium described as potential human fecal pollution indicators were found in domestic animals. In this study under the environmental and experimental conditions evaluated was not possible to find a Bifidobacterium species as specific marker of human fecal contamination in tropical areas. However, the applied method in this study could be useful to detect fecal pollution in tropical waters allowing a nearest approximation to the origin of the fecal pollution compared with cultural traditional methods, since it was possible to find identical DNA sequences in the water and in the fecal samples.

Bacterial community dynamics during bioremediation of alkane- and PAHs-contaminated soil of Siri island, Persian Gulf: a microcosm study

Studding the diversity of soil indigenous microorganisms, and monitoring effect of contaminants on microbial population, is very critical for understanding microbial activity during bioremediation and selecting successful remediation strategy. To simulate the natural environment, four microcosms were prepared by artificially contaminating clean soil with defined amounts of petroleum hydrocarbons including alkanes mixture (C13–C20), polyaromatic hydrocarbons (PAHs) mixture (anthracene, phenanthrene, fluoranthene, pyrene and benzo (α) pyrene) and both alkanes and PAHs. Contaminants degradation and heterotrophic bacterial count were measured during a 6-month study. Copy number of alkB and C23DO genes was studied using real-time PCR, and bacterial diversity was monitored by 16S rRNA gene PCR and denaturing gradient gel electrophoresis (DGGE). Results indicated that all types of contaminants (except the five ring benzo (α) pyrene) were totally degraded after 6 months and the increase in hydrocarbon degradation rate coincided with the enhancement of total heterotrophic bacterial count in each microcosm. Real-time PCR results showed a significant increase in the copy number of both alkB and C23DO genes in alkane- and PAHs-contaminated microcosm comparing with the control microcosm, indicating selection for special hydrocarbon degraders in hydrocarbon-amended microcosms. The results of DGGE revealed that the type of contaminant in the same soil has a remarkable influence on soil bacterial community structure. Sequencing of DGGE bands suggested that most of the dominant members of the microbial community of contaminated soil are unculturable bacteria from Proteobacteria and the genus Bacillus.

Spatial variations in intestinal skatole production and microbial composition in broilers.

Spatial variations in intestinal skatole production and microbial composition in broilers were evaluated. Fifteen 42-day-old broilers were slaughtered. Samples were taken from the broilers' ileum, cecum, and rectum and analyzed for skatole levels. Denaturing gradient gel electrophoresis (DGGE) technique was used to analyze the microbial community from the intestinal digesta. The skatole levels could be arranged in decreasing order: cecum>rectum>ileum. Cecal lactate and acetate levels were higher than those of ileum and rectum (p<0.01). Cecal microbial diversity and richness were higher than those of ileum (p<0.05). One specific DGGE band was found in cecal sample and is closely related to Bacteroides uniformis. Cecum and rectum samples consisted of three coexistence bands, the related bacteria included Lactobacillus vaginalis and two members of Candidatus Arthromitus. The total bacterial population in cecum was higher than that in ileum and rectum (p<0.05). Skatole levels were positively correlated with microbial Shannon-Wiener index, richness, total bacteria (p<0.01) and Lactobacilli and Bifidobacterium (p<0.05) populations. These results suggest that the variations in fermentation patterns are more likely to explain differences in intestinal skatole level. Bacteroides uniformis may play a role in the production of skatole.

Microbial community changes induced by Managed Aquifer Recharge activities: linking hydrogeological and biological processes

Abstract. Managed Aquifer Recharge (MAR) is a technique used worldwide to increase the availability of water resources. We study how MAR modifies microbial ecosystems and its implications for enhancing biodegradation processes to eventually improve groundwater quality. We compare soil and groundwater samples taken from a MAR facility located in NE Spain during recharge (with the facility operating continuously for several months) and after 4 months of no recharge. The study demonstrates a strong correlation between soil and water microbial prints with respect to sampling location along the mapped infiltration path. In particular, managed recharge practices disrupt groundwater ecosystems by modifying diversity indices and the composition of microbial communities, indicating that infiltration favors the growth of certain populations. Analysis of the genetic profiles showed the presence of nine different bacterial phyla in the facility, revealing high biological diversity at the highest taxonomic range. In fact, the microbial population patterns under recharge conditions agree with the intermediate disturbance hypothesis (IDH). Moreover, DNA sequence analysis of excised denaturing gradient gel electrophoresis (DGGE) band patterns revealed the existence of indicator species linked to MAR, most notably Dehalogenimonas sp., Nitrospira sp. and Vogesella sp.. Our real facility multidisciplinary study (hydrological, geochemical and microbial), involving soil and groundwater samples, indicates that MAR is a naturally based, passive and efficient technique with broad implications for the biodegradation of pollutants dissolved in water.

Diversity and seasonal distribution of ammonia-oxidizing archaea in the water column of a tropical estuary along the southeast Arabian Sea.

Diversity and distribution pattern of ammonia-oxidizing archaea (AOA) were studied across a salinity gradient in the water column of Cochin Estuary (CE), a tropical monsoonal estuary along the southeast Arabian Sea. The water column of CE was found to be nutrient rich with high bacterial (3.7-6.7 × 108cellsL-1) and archaeal abundance (1.9-4.5 × 108cellsL-1). Diversity and seasonal variation in the distribution pattern of AOA were studied using clone library analysis and Denaturing gradient gel electrophoresis (DGGE). Clone library analysis of both the amoA and 16S rRNA gene sequences showed similar diversity pattern, however the diversity was more clear when the 16S rRNA gene sequences were analyzed. More than 70% of the sequences retrieved were clustered under uncultured Thaumarchaeota group 1 lineage and the major fractions of the remaining sequences were grouped into the Nitrosopumilus lineage and Nitrosopelagicus lineage. The AOA community in the CE was less adaptable to changing environmental conditions and its distribution showed seasonal variations within the DGGE banding pattern with higher diversity during the pre-monsoon period. The distribution of AOA also showed its preference to intermediate salinity for their higher diversity. Summer monsoon associated runoff and flushing played a critical role in regulating the seasonality of AOA distribution.

Effects of thymol and carvacrol, alone or in combination, on fermentation and microbial diversity during in vitro culture of bovine rumen microbes

Two essential oils (EO), thymol and carvacrol, were used in six ratio (100:00, 80:20, 60:40, 40:60, 20:80 and 00:100) combinations of both EO and in a dose of 0.2 g L−1 in bovine ruminal culture medium, 24-h cultures, to evaluate effects on total gas production (TGP), methane production, in vitro dry matter digestibility (IVDMD) and in vitro culture population dynamics of methanogenic and total bacteria. Total DNA extracted from ruminal microorganisms was subjected to denaturing gradient gel electrophoresis (DGGE)-polymerase chain reaction (PCR) to examine effects on bacterial populations. The effect of EO on TGP and IVDMD were assessed by comparison to untreated control cultures. In general, methane production by the microbial populations appeared to be higher with treatments containing the highest concentration of thymol than with treatments containing more carvacrol resulting in a tendency for greater methane-inhibiting activity achieved as the thymol concentration in the thymol:carvacrol mixtures decreased linearly. The population of total bacteria with a 74.5% Dice similarity coefficient for comparison of DGGE band patterns indicating shifts in bacterial constituents as EO ratios changed. No effects on TGP, IVDMD while only slight shifts in the methanogenic populations were seen with an overall 91.5% Dice similarity coefficient.

Alphaproteobacteria communities depend more on soil types than land managements

ABSTRACTSoil properties and agricultural practices take a joint effect on the communities of soil bacteria. The aim of the present study was to survey Alphaproteobacterial communities as possible indicators of soil quality considering clay, loamy and sandy soils under conventional and organic farming. Alphaproteobacteria community composition were analysed by 16S rRNA gene with nested-PCR (polymerase chain reaction) and denaturing gradient gelelectrophoresis (DGGE). Sequencing of partial 16S rRNA gene from the DGGE bands were performed. Conventional and organic farming resulted in significant differences in chemical properties of soils. According to the results community fingerprints were separated into groups depending on soil types and farming systems. This separation can be attributed mostly to soil pH, AL-P2O5,-K2O. The analysed sequences were identified as soil bacteria which could play the main role in nitrogen fixing, mineralisation and denitrification. The highest diversity index was revealed from the organic farming at sandy texture site, where mainly Mesorhizobium sp. and Rhizobium sp. were detected. The soil type and actual crop could have a stronger impact on the soil bacterial composition than the management.

Diversity of urinary tract infection bacteria in children in Indonesia based on metagenomic approach

Christine G, Budiarti S, Astuti RI. 2018. Diversity of urinary tract infection bacteria in children in Indonesia based on metagenomic approach. Biodiversitas 19: 1375-1381. Urinary tract infection (UTI) is a common bacterial infection in childhood in both males and females. The infection is usually caused by bacterial invasion of the urinary tract including the lower and the upper urinary tract. In Indonesia, to the best our knowledge, the diversity of urinary tract infection bacteria has not been reported yet. Therefore, the aims of this study were to identify the diversity of both culturable and unculturable bacteria in children diagnosed with UTI. In this study, urine samples were obtained from different age groups ranging 6-17 years. Analysis of 16S rRNA gene sequence showed eight culturable isolates (SBU1, SBU2, SBU3, SBU4, SBU5, SBU6, SBU7, SBU8) are closely related to Escherichia coli, Klebsiella pneumoniae, Enterobacter aerogenes, Citrobacter sp. and Acinetobacter sp. with maximum identity up to 98-99%. Diversity of unculturable bacteria community based on 16S rRNA gene was represented by 9 DGGE (Denaturing Gradient Gel Electrophoresis) bands. The nine respective bands showed the similarity ranging from 84 up to 96% with Klebsiella sp, Escherichia sp., Lactococcus lactic, Shigella flexneri and uncultured bacterium. Based on phylogenetic analysis, all culturable isolates belong to phylum Proteobacteria, which is dominated by family of Enterobacteriaceae. Interestingly, by using metagenomic approach, it is observed that bacteria belong to phylum Firmicutes were found in the UTI-diagnosed patients, in addition to those bacterial isolates from phylum Proteobacteria. To our knowledge, this is the first study to report the occurrence of Firmicutes and Proteobacteria in UTI-diagnosed patients in Indonesia.

The effect of bacterial and archaeal populations on anaerobic process fed with mozzarella cheese whey and buttermilk

Dairy wastes can be conveniently processed and valorized in a biorefinery value chain since they are abundant, zero-cost and all year round available. For a comprehensive knowledge of the microbial species involved in producing biofuels and valuable intermediates from dairy wastes, the changes in bacterial and archaeal population were evaluated when H2, CH4 and chemical intermediates were produced. Batch anaerobic tests were conducted with a mixture of mozzarella cheese whey and buttermilk as organic substrate, inoculated with 1% and 3% w/v industrial animal manure pellets. The archaeal methanogens concentration increased in the test inoculated at 3% (w/v) when H2 and CH4 production occurred, being 1 log higher than that achieved in the test inoculated at 1% (w/v). Many archaeal species, mostly involved in the production of CH4, were identified by sequencing denaturing gradient gel electrophoresis (DGGE) bands. Methanoculleus, Methanocorpusculum and Methanobrevibacter genera were dominant archaea involved in the anaerobic process for bioenergy production from mozzarella cheese whey and buttermilk mixture.

Brain-derived neurotrophic factor preserves intestinal mucosal barrier function and alters gut microbiota in mice

The intestinal mucosal barrier (IMB) enables the intestine to provide adequate containment of luminal microorganisms and molecules while preserving the ability to absorb nutrients. In this study, we explored the effect of brain-derived neurotrophic factor (BDNF) on IMB function and gut microbiota in mice. BDNF gene knock-out mice (the BDNF+/− group) and wild-type mice (the BDNF+/+ group) were selected. The gut microbiota of these mice was analyzed by denaturing gradient gel electrophoresis (DGGE) assay. The ultrastructure of the ileum and the colonic epithelium obtained from decapitated mice were observed by transmission electron microscopy. The protein expression of epithelial tight junction proteins, zonula occludens-1 (ZO-1) and occludin was detected by immunohistochemistry staining. The protein expression of claudin-1 and claudin-2 was determined by Western blotting. The DGGE band patterns of gut microbiota in the BDNF+/− group were significantly different from that in the BDNF+/+ group, which indicated that the BDNF expression alters the gut microbiota in mice. Compared with the BDNF+/+ group, the BDNF+/− group presented no significant difference in the ultrastructure of ileal epithelium; however, a significant difference was observed in the colonic epithelial barrier, manifested by decreased microvilli, widening intercellular space and bacterial invasion. Compared with the BDNF+/+ group, the expression of ZO-1 and occludin in the BDNF+/− group was significantly decreased. The expression of claudin-1 in the BDNF+/− group was significantly reduced, while the expression of claudin-2 was elevated. These findings indicate that BDNF preserves IMB function and modulates gut microbiota in mice.

Cyanobacterial community diversity in the sediments of the Pearl River Estuary in China

Cyanobacterial community diversity in the sediment of the Pearl River Estuary in China was evaluated in this study by denaturing gradient gel electrophoresis (DGGE) during the wet and dry seasons. Nucleotide sequences obtained from DGGE bands were classified into five cyanobacterial clusters, including Synechococcus, Cyanobium, Chroococcus, Prochlorales and Tolypothrix. Synechococcus was identified as the dominant cyanobacterial group in the sediment samples; its distribution varied from the inner estuary to the outer estuary, with a wide range of salinity adaptation. Observed patterns of cyanobacterial communities changed markedly between sampling sites and seasons, suggesting that most cyanobacteria were not delivered via fresh water. Canonical correspondence analysis was conducted to determine the relationship between environmental variables and bacterial community structures during the dry season. The results suggested that the cyanobacterial community was significantly influenced by pH, salinity, PO4-P and NO3-N in sediments.