Denaturing Gradient Gel Electrophoresis Banding Patterns Research Articles

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.

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.

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.

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.

Effects of kelp Ecklonia maxima inclusion in formulated feed on the growth, feed utilisation and gut microbiota of South African abalone Haliotis midae

The effect of kelp Ecklonia maxima inclusion in formulated feeds on abalone growth and gut bacterial communities has not been previously investigated in South Africa. An eight-month on-farm growth trial was conducted with sub-adult Haliotis midae (∼43 mm shell length) fed graded levels of kelp in formulated feeds. Kelp inclusion (0.44–3.54% of pellet dry mass) promoted faster growth (65.7–74.5% total mass gain), with better feed and protein conversions (apparent feed conversion ratio [FCR] 1.4–1.8, apparent protein efficiency ratio [PER] 2.3–2.7), as compared with the non-supplemented feed (52.3% total mass gain, FCR 2.1, PER 1.9; p < 0.001). Abalone-gut bacterial DNA was sequenced using 16S rRNA gene pyrosequencing and the sequences were clustered into operational taxonomic units (OTUs) at a 97% similarity level. A supplementary 16S rRNA gene denaturing gradient gel electrophoresis (DGGE) analysis was employed. The dominant OTUs differed in terms of their relative abundances, with an autochthonous Mycoplasma strain being significantly more abundant (p = 0.03) in the gut of abalone fed a kelp-supplemented feed. The DGGE band patterns displayed higher within-group variability for abalone fed the control diet, suggesting that dietary kelp inclusion promotes gut-bacteria homeostasis. This may contribute to better feed utilisation and growth in abalone fed kelp-supplemented feeds.

Assessment of cecal microbiota, integron occurrence, fermentation responses, and Salmonella frequency in conventionally raised broilers fed a commercial yeast-based prebiotic compound

Prebiotics are defined as nondigestible food ingredients that can stimulate the growth of one or more beneficial bacteria in the gastrointestinal tract. The Biolex® MB40 is a commercial prebiotic that contains mannanoligosaccharides. The aims of this study were to evaluate the effects of prebiotic Biolex® MB40 on cecal microbiota of conventionally raised chickens using PCR-based denaturing gradient gel electrophoresis (DGGE) and assessing Salmonella prevalence. Chickens were randomly selected and distributed into three groups; a negative control (NC) and two treatment groups (T1 and T2). The NC group was fed a non-medicated feed, while the treatment groups were fed either T1 or T2, 0.05% antibiotic (BMD50) or 0.2% Biolex® MB40 respectively. During the study, cecal contents and bird feed were plated on selective media for Salmonella, yeast and mold prevalence analysis. Ten chickens from each group were randomly selected at 1, 2, 4 and 6 wk and ceca were extracted for DNA isolation for PCR-based DGGE. Also, short-chain fatty acids (SCFAs) were analyzed from collected cecal material by gas chromatography. Only 4.2% of the samples were Salmonella positive. Presence of class 1 integron from cecal material were analyzed by PCR and 97.5% of the cecal samples were positive for integron presence, but no class I integrons were detected in the Salmonella isolates. According to the PCR-based DGGE analysis, the T2 group exhibited a cecal microbial population pattern that was similar to the T1 group prior to wk 4 and the T2 group appeared to be almost identical with the NC group after wk 4 but T2 exhibited less Bacteroides rodentium prior to wk 4. Overall results showed that the commercial prebiotic, MB40 did not lead to a detectable reduction of Salmonella but the general frequency of Salmonella was minimal in all treatments. However, feeding an MB40 supplement did result in similar DGGE band patterns as the T1 group indicating that cecal microbiotia were potentially similar in these 2 groups. Overall, it appears that MB40 (T2) exhibited similar DGGE-cecal population patterns as BMD50 (T1) which suggests that these treatments may have influenced the populations in a comparable fashion.

Assessment of Soil Microbial Communities in Carotenoid-Biofortified Rice Ecosystem

This study was conducted to investigate the effect of Psy-2A-CrtI (PAC), a genetically modified (GM) rice with enhanced <TEX>${\beta}$</TEX>-carotene, on the soil microbial community. The soil used to cultivate GM rice and its wild-type, Nakdong, was analyzed for population density, denaturing gradient gel electrophoresis (DGGE), and pyrosequencing. It was found that the bacterial, fungal and actinomycetes population densities of the PAC soils were within the range of those of the non-GM rice cultivar, Nakdong. The DGGE banding patterns of the GM and non-GM soils were also similar, suggesting that the bacterial community structures were stable within a given month and were unaffected by the presence of a GM plant. The pyrosequencing result showed a temporal difference in microorganism taxon and distribution ratio, but no significant difference between GM and non-GM was found. The persistence of the transgene DNA in the plant and surrounding soil were investigated for different time periods. There were differences in the persistence within the plant depending on the gene, but they could not be detected after 5 weeks. Also the transgenes were not detected in the surrounding soil. These results indicate that soil microbial communities are unaffected by the cultivation of a PAC rice within the experimental time frame.

Effect of genetically modified rice producing resveratrol on the soil microbial communities

Cultivation of genetically modified (GM) crops has rapidly increased in the global agricultural area. However, cultivation of GM crops in the field evoked the concern of the possibility of unintentional consequences from transgenic plant into environment. In our present study, we have assessed the effects of RS526, GM rice producing resveratrol on the surrounding soil microbial community. The effects of RS526 on the soil microbial community in its field of growth were assessed using a conventional culture technique and culture-independent molecular methods. Three replicate field plots were planted with single GM rice and a non-GM counterpart, Dongjin. The soil microbial communities around these plants were compared using colony counting, denaturing gradient gel electrophoresis (DGGE), pyrosequencing analysis, and community-level physiological profiling during the growing periods. The bacterial, fungal, and actinomycetes population densities of the RS526 soils were found to be within the range of those of the non-GM rice cultivar. The DGGE banding patterns of the GM and non-GM soils were also similar, suggesting that the bacterial community structures were stable within a given month and were unaffected by the presence of a GM plant. The data obtained from pyrosequencing analysis showed that the bacterial community distribution at the phylum level were highly similar to DGGE patterns between two tested groups. The substrate utilization pattern of RS526 and Dongjin rice soil was quite similar between each sampling time. These results indicate that soil microbial communities are not significantly affected by the cultivation of RS526 within the experimental time frame.

Microbial Distribution in a Hydrothermal Plume of the Southwest Indian Ridge

abstractHydrothermal plumes are widely distributed throughout the global spreading ridges, yet few of them are microbiologically explored. The ultraslow-spreading ridges, recently recognized as a unique, new class of mid-ocean-ridge system, have provided surprises and new insights in hydrothermal system research. A suite of water column samples including both hydrothermal plume samples and ambient seawater were collected at different depths from the ultraslow-spreading Southwest Indian Ridge (SWIR) in 2010. We use molecular approaches such as clone libraries, denaturing gradient gel electrophoresis (DGGE) and quantitative PCR to determine microbial community compositions and their spatial variability within the hydrothermal plume and seawater. Phylogenetic analysis showed that plume samples were mainly dominated by members of α-Proteobacteria and γ-Proteobacteria and members of marine group I group within the Crenarchaeota. Within the hydrothermal plume, archaeal populations were spatially homogeneous, while bacterial compositions were heterogeneous and remarkably distinct at different depths. Moreover, several lineages, closely related to known Mn(II) oxidizers were found to be abundant and even predominant within the plume bacterial communities. DGGE band patterns showed that there was no significant difference in microbial compositions between the samples of hydrothermal plume and ambient seawater. Taken together, we inferred that microbial communities in the SWIR hydrothermal plumes were sourced from ambient seawater rather than from seafloor vent-derived niches. This is the first report on the characteristics of microbial community structures in hydrothermal plume and ambient seawater in the Southwest Indian Ridge.

Biological sulphide removal from anaerobically treated domestic sewage: reactor performance and microbial community dynamics

We developed a biological sulphide oxidation system and evaluated two reactors (shaped similar to the settler compartment of an up-flow anaerobic sludge blanket [UASB] reactor) with different support materials for biomass retention: polypropylene rings and polyurethane foam. The start-up reaction was achieved using microorganisms naturally occurring on the open surface of UASB reactors treating domestic wastewater. Sulphide removal efficiencies of 65% and 90% were achieved with hydraulic retention times (HRTs) of 24 and 12 h, respectively, in both reactors. However, a higher amount of elemental sulphur was formed and accumulated in the biomass from reactor 1 (20 mg S0 g−1 VTS) than in that from reactor 2 (2.9 mg S0 g−1 VTS) with an HRT of 24 h. Denaturing gradient gel electrophoresis (DGGE) results revealed that the the pink and green biomass that developed in both reactors comprised a diverse bacterial community and had sequences related to phototrophic green and purple-sulphur bacteria such as Chlorobium sp., Chloronema giganteum, and Chromatiaceae. DGGE band patterns also demonstrated that bacterial community was dynamic over time within the same reactor and that different support materials selected for distinct bacterial communities. Taken together, these results indicated that sulphide concentrations of 1–6 mg L−1 could be efficiently removed from the effluent of a pilot-scale UASB reactor in two sulphide biological oxidation reactors at HRTs of 12 and 24 h, showing the potential for sulphur recovery from anaerobically treated domestic wastewater.

Factors shaping bacterial phylogenetic and functional diversity in coastal waters of the NW Mediterranean Sea

To evaluate the main factors shaping bacterioplankton phylogenetic and functional diversity in marine coastal waters, we carried out a two-year study based on a monthly sampling in Blanes Bay (NW Mediterranean). We expected the key factors driving bacterial diversity to be (1) temperature and nutrient concentration, together with chlorophyll a concentration as an indicator of phytoplankton biomass and, hence, a carbon source for bacteria (here called bottom-up factors), and (2) top-down pressure (virus- and protist-mediated mortality of bacteria). Phylogenetic diversity was analyzed by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA. Functional diversity was assessed by using monomeric carbon sources in Biolog EcoPlates and by determining the activity of six extracellular enzymes. Our results indicate that the bacterial phylogenetic and functional diversity in this coastal system is shaped mainly by bottom-up factors. A dendrogram analysis of the DGGE banding patterns revealed three main sample clusters. Two clusters differed significantly in temperature, nitrate and chlorophyll a concentration, and the third was characterized by the highest losses of bacterial production due to viral lysis detected over the whole study period. Protistan grazing had no effect on bacterial functional diversity, since there were no correlations between protist-mediated mortality (PMM) and extracellular enzyme activities, and utilization of only two out of the 31 carbon sources (N-acetyl-d-glucosamine and α-cyclodextrin) was correlated with PMM. In contrast, virus-mediated mortality correlated with changes in the percentage of use of four carbon sources, and also with specific leu-aminopeptidase and β-glucosidase activity. This suggests that viral lysate provides a pool of labile carbon sources, presumably including amino acids and glucose, which may inhibit proteolytic and glucosidic activity. Our results indicate that bottom-up factors play a more important role than top-down factors (i.e. viral lysis and protistan grazing) in shaping bacterial community structure and activity. Furthermore, they suggest that viruses play a more important role than protists in modifying community structure and functional diversity of bacteria in oligotrophic marine coastal waters.

Bacterial communities in alfalfa and corn silages produced in large‐scale stack and bunker silos in China

AbstractAlfalfa silage (Al) and corn silage (Cs) samples were collected from two large‐scale farms in China; one of these farms used stack silos and the other used bunker silos for silage production. Three samples were collected from the upper and lower layers of each silo. Thus, six samples were examined for each of Al‐stack, Al‐bunker, Cs‐stack, and Cs‐bunker. Bacterial community was determined by denaturing gradient gel electrophoresis (DGGE). Lactic acid was the main fermentation product in Al‐stack, Cs‐stack and Cs‐bunker, whereas acetic acid and butyric acid were predominant in Al‐bunker. Pediococcus pentosaceus and Clostridium sp. were common to four silage types. Lactobacillus acetotolerans and Lactobacillus pontis were detected specifically in Cs, whereas the lactic acid bacteria identified in Al were regarded as those usually found in silage. Differences between stack and bunker silos were apparent in Al with regard to fermentation products and DGGE band patterns. Differences between the upper and lower layers were observed in the fermentation products in Cs regardless of silo type, whereas variations in the DGGE band patterns of Cs‐stack were detected.

Key design factors affecting microbial community composition and pathogenic organism removal in horizontal subsurface flow constructed wetlands

Constructed wetlands constitute an interesting option for wastewater reuse since high concentrations of contaminants and pathogenic microorganisms can be removed with these natural treatment systems. In this work, the role of key design factors which could affect microbial removal and wetland performance, such as granular media, water depth and season effect was evaluated in a pilot system consisting of eight parallel horizontal subsurface flow (HSSF) constructed wetlands treating urban wastewater from Les Franqueses del Vallès (Barcelona, Spain). Gravel biofilm as well as influent and effluent water samples of these systems were taken in order to detect the presence of bacterial indicators such as total coliforms (TC), Escherichia coli, fecal enterococci (FE), Clostridium perfringens, and other microbial groups such as Pseudomonas and Aeromonas. The overall microbial inactivation ratio ranged between 1.4 and 2.9 log-units for heterotrophic plate counts (HPC), from 1.2 to 2.2 log units for total coliforms (TC) and from 1.4 to 2.3 log units for E. coli. The presence of fine granulometry strongly influenced the removal of all the bacterial groups analyzed. This effect was significant for TC (p=0.009), E. coli (p=0.004), and FE (p=0.012). Shallow HSSF constructed wetlands were more effective for removing Clostridium spores (p=0.039), and were also more efficient for removing TC (p=0.011) and E. coli (p=0.013) when fine granulometry was used. On the other hand, changes in the total bacterial community from gravel biofilm were examined by using denaturing gradient gel electrophoresis (DGGE) and sequencing of polymerase chain reaction (PCR)-amplified fragments of the 16S rRNA gene recovered from DGGE bands. Cluster analysis of the DGGE banding pattern from the different wetlands showed that microbial assemblages separated according to water depth, and sequences of different phylogenetic groups, such as Alpha, Beta and Delta-Proteobacteria, Nitrospirae, Bacteroidetes, Acidobacteria, Firmicutes, Synergistetes and Deferribacteres could be retrieved from DGGE bands.

Insights into aerobic microbial community in the Kamniška Bistrica river sediment with culture-dependent and molecular biology approach

River systems are exposed to anthropogenic disturbances, including chemical pollution and eutrophication. They may affect a structure and diversity of microbial communities in river sediment. The aim of the study was to describe diversity and structure of a bacterial community in the Kamniška Bistrica river sediment using culture-dependent and molecular methods. Sediment samples were collected from three sampling stations along the Kamniška Bistrica river: upstream (Kamniška Bistrica), midstream (Vir) and downstream (Bišče), and physico-chemical analysis was conducted on-site. Isolates were recovered from three different agar plate media (LB, NB in R2A) and micro- as well as macromorphologically described. DNA was extracted from pure cultures and directly from sediment samples, and 16S rRNA gene segments were PCR amplified using universal bacterial primers. The PCR products were subjected to denaturing gradient gel electrophoresis (DGGE). The results showed that the DGGE was an appropriate method for monitoring the changes in the community structure of the river sediment and allows to determine the impact of environmental factors on bacterial diversity. The comparative analysis of the DGGE profiles from isolates and sediment samples showed that the DGGE banding patterns revealed different bacterial community structures for all three sampling stations, while the DGGE profiles of isolates did not represent dominant bacterial populations of the sediment. On the bases of the DGGE profiles, 25 isolates were chosen and their 16S rRNA genes were amplified and sequenced. All partial nucleotide sequences of 16S rRNA genes were preleminary taxonomically identified by using BLAST. The majority of sequenced isolates belonged to bacteria normally present in aquatic environments.

Vertical distribution of methane oxidation and methanotrophic response to elevated methane concentrations in stratified waters of the Arctic fjord Storfjorden (Svalbard, Norway)

Abstract. The bacterially mediated aerobic methane oxidation (MOx) is a key mechanism in controlling methane (CH4) emissions from the world's oceans to the atmosphere. In this study, we investigated MOx in the Arctic fjord Storfjorden (Svalbard) by applying a combination of radio-tracer-based incubation assays (3H-CH4 and 14C-CH4), stable C-CH4 isotope measurements, and molecular tools (16S rRNA gene Denaturing Gradient Gel Electrophoresis (DGGE) fingerprinting, pmoA- and mxaF gene analyses). Storfjorden is stratified in the summertime with melt water (MW) in the upper 60 m of the water column, Arctic water (ArW) between 60 and 100 m, and brine-enriched shelf water (BSW) down to 140 m. CH4 concentrations were supersaturated with respect to the atmospheric equilibrium (about 3–4 nM) throughout the water column, increasing from ∼20 nM at the surface to a maximum of 72 nM at 60 m and decreasing below. MOx rate measurements at near in situ CH4 concentrations (here measured with 3H-CH4 raising the ambient CH4 pool by &lt;2 nM) showed a similar trend: low rates at the sea surface, increasing to a maximum of ∼2.3 nM day−1 at 60 m, followed by a decrease in the deeper ArW/BSW. In contrast, rate measurements with 14C-CH4 (incubations were spiked with ∼450 nM of 14C-CH4, providing an estimate of the CH4 oxidation at elevated concentration) showed comparably low turnover rates (&lt;1 nM day−1) at 60 m, and peak rates were found in ArW/BSW at ∼100 m water depth, concomitant with increasing 13C values in the residual CH4 pool. Our results indicate that the MOx community in the surface MW is adapted to relatively low CH4 concentrations. In contrast, the activity of the deep-water MOx community is relatively low at the ambient, summertime CH4 concentrations but has the potential to increase rapidly in response to CH4 availability. A similar distinction between surface and deep-water MOx is also suggested by our molecular analyses. The DGGE banding patterns of 16S rRNA gene fragments of the surface MW and deep water were clearly different. A DGGE band related to the known type I MOx bacterium Methylosphaera was observed in deep BWS, but absent in surface MW. Furthermore, the Polymerase Chain Reaction (PCR) amplicons of the deep water with the two functional primers sets pmoA and mxaF showed, in contrast to those of the surface MW, additional products besides the expected one of 530 base pairs (bp). Apparently, different MOx communities have developed in the stratified water masses in Storfjorden, which is possibly related to the spatiotemporal variability in CH4 supply to the distinct water masses.

A flat microbial fuel cell for decentralized wastewater valorization: process performance and optimization potential

A very compact flat microbial fuel cell (MFC), with 64 cm2 each for the anode surface and the cathode surface and 1 cm3 each for the anode and cathode chambers, was tested for wastewater treatment with simultaneous electricity production with the ultimate goal of implementing an autonomous service in decentralized wastewater treatment systems. The MFC was operated with municipal wastewater in sequencing batch reactor mode with re-circulation. Current densities up to 407 W/m3 and a carbon removal of 83% were obtained. Interruption in the operation slightly decreased power density, while the re-circulation ratio did not influence power generation. The anode biofilm presented high conductivity, activity and diversity. The denaturing gradient gel electrophoresis band-pattern of the DNA showed the presence of several ribotypes with different species of Shewanellaceae and Geobacteraceae families.

The microbiome of North Sea copepods

Copepods can be associated with different kinds and different numbers of bacteria. This was already shown in the past with culture-dependent microbial methods or microscopy and more recently by using molecular tools. In our present study, we investigated the bacterial community of four frequently occurring copepod species, Acartia sp., Temora longicornis, Centropages sp. and Calanus helgolandicus from Helgoland Roads (North Sea) over a period of 2 years using DGGE (denaturing gradient gel electrophoresis) and subsequent sequencing of 16S-rDNA fragments. To complement the PCR-DGGE analyses, clone libraries of copepod samples from June 2007 to 208 were generated. Based on the DGGE banding patterns of the two years survey, we found no significant differences between the communities of distinct copepod species, nor did we find any seasonality. Overall, we identified 67 phylotypes (>97 % similarity) falling into the bacterial phyla of Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. The most abundant phylotypes were affiliated to the Alphaproteobacteria. In comparison with PCR-DGGE and clone libraries, phylotypes of the Gammaproteobacteria dominated the clone libraries, whereas Alphaproteobacteria were most abundant in the PCR-DGGE analyses.

Effect of organic, conventional and mixed cultivation practices on soil microbial community structure and nematode abundance in a cultivated onion crop

Responses of the soil microbial and nematode community to organic and conventional agricultural practices were studied using the Teagasc Kinsealy Systems Comparison trial as the experimental system. The trial is a long-term field experiment which divides conventional and organic agriculture into component pest-control and soil treatment practices. We hypothesised that management practices would affect soil ecology and used community level physiological profiles, microbial and nematode counts, and denaturing gradient gel electrophoresis (DGGE) to characterise soil microbial communities in plots used for onion (Allium cepa L.) cultivation. Microbial activity and culturable bacterial counts were significantly higher under fully organic management. Culturable fungi, actinomycete and nematode counts showed a consistent trend towards higher numbers under fully organic management but these data were not statistically significant. No differences were found in the fungal/bacterial ratio. DGGE banding patterns and sequencing of excised bands showed clear differences between treatments. Putative onion fungal pathogens were predominantly sequenced under conventional soil treatment practices whilst putative soil suppressive bacterial species were predominantly sequenced from the organic pest-control treatment plots. Organic management increased microbial activity and diversity. Sequence data was indicative of differences in functional groups and warrants further investigation.

Diversity of bacterial community during spring phytoplankton blooms in the central Yellow Sea

Bacterial community diversity and the effects of environmental factors on bacterial community composition during 2 spring phytoplankton blooms in the central Yellow Sea were investigated by using denaturing gradient gel electrophoresis (DGGE) and multivariate statistical analysis. The Shannon-Weaver indices (H') of bacterial diversity from samples at station B23 were higher than those at station B20. Cluster analysis based on DGGE band patterns indicated temporal variations of bacterial community at the 2 bloom stations but a vertical distribution pattern only at station B20. The predominant bacterial groups were affiliated with Alphaproteobacteria, Gammaproteobacteria, Cytophaga-Flavobacterium-Bacteroides, Deltaproteobacteria, and Actinobacteria. The effects of environmental factors on bacterial community were analyzed by canonical correspondence analysis. Bacterial community structures were significantly affected by silicate at station B20 and by Paralia sulcata and Heterocapsa spp. at station B23. From the results, phytoplankton species composition had a significant effect on bacterial community structure during phytoplankton blooms in the central Yellow Sea.