PCR-DGGE Fingerprinting Research Articles

Probiotic supplementation in systemic nickel allergy syndrome patients: study of its effects on lactic acid bacteria population and on clinical symptoms.

The study aimed to evaluate the effects of probiotic Lactobacillus reuteri DSM 17938 strain supplementation in patients suffering from systemic nickel allergy syndrome, in terms of modulation of faecal LAB population linked to a reduction of GI and cutaneous symptoms and to an increase of patient's quality of life. A preliminary double-blind randomized placebo-controlled study was planned and a culture-independent method based on denaturing gradient gel electrophoresis (DGGE) analysis coupled to the 16S rRNA gene sequencing was applied to investigate on the dynamics of faecal LAB communities before and during a low-Ni diet, supplemented with the probiotic strain. Moreover, the severity and the frequency of GI and cutaneous reactions as well as patient's clinical condition perception (VAS scores) were estimated by statistical analysis. PCR-DGGE fingerprinting obtained using LAB-specific primers revealed significant shift in faecal community with an increase in biodiversity in patients supplemented with probiotic Lact.reuteri strain. In addition, GI reactions such as symptoms related to meals and type of stools significantly improved only in patients treated with Lact.reuteri, while severity and frequency of cutaneous symptoms (urticaria, itch and eczema) and recurrent abdominal pain (RAP) as well as VAS scores statistically decreased in both groups. Our preliminary findings suggest that probiotic Lact.reuteri could be a useful supplementation during a low-Ni diet of patients with SNAS, to increase LAB population diversity, which could contribute to restore the intestinal homoeostasis conditions. To date, no information is available on probiotics application and on their effects, in terms of intestinal microbiota modulation, on patients suffering from SNAS. Therefore, the identification of dominant LAB community and the study of its shift during the probiotic supplementation could enhance the knowledge of the SNAS syndrome.

Evaluation of relationship between Chilean octopus (Octopus mimusGould, 1852) egg health condition and the egg bacterial community

The objective of this study was to evaluate how bacterial community associated with Chilean octopus (Octopus mimus) egg was related to egg health condition using a culture dependent method and PCR-DGGE fingerprinting technique. Total heterotrophic bacterial number of fresh egg was much lower than infected egg. However, biodiversity of culturable bacterial community associated with the fresh egg exhibited a higher diversity than the infected egg. Result of a culture dependent method showed that Roseobacter clade was predominant in the fresh egg, while predominant species in the infected egg was γ-proteobacteria. DGGE fingerprinting technique showed that fresh egg associated unculturable bacterial community was constituted of Roseobacter clade and Bacteroidetes, whereas Bacteroidetes was predominant bacteria in the infected egg. These results suggest that there might be some sort of relationship between octopus eggs associated bacterial community and egg health condition. Moreover, Roseobacter clade and Bacteroidetes might be potential symbiotic bacteria associated with the octopus egg, and some γ-proteobacteria might be involved in octopus egg disease. In particular, Roseobacter clade may play an important role in octopus egg health and it raises the possibility that this clade can be utilized as potential probiotics for octopus aquaculture.

Spatiotemporal pattern of bacterioplankton in Donghu Lake

Bacterioplankton play key roles in the biogeochemical cycle and in organic contaminant degradation. The species richness and abundance of bacterial subgroups are generally distinct from each other, and this is attributed to their different functions in aquatic ecosystems. The spatiotemporal variations of eight phylogenetic subgroups (Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, Planctomycetes, alpha-, beta-, and gamma-Proteobacteria) derived from Donghu Lake were investigated using PCR-DGGE fingerprinting, to explore their responses to environmental factors. Results indicate that Actinobacteria and beta-Proteobacteria were the two largest bacterial subgroups detected. These two groups and Bacteroidetes showed clear seasonal patterns in composition of the operational taxonomic unit. Results also suggest that the bacterioplankton subgroups in Donghu Lake were significantly correlated with different environmental factors. In brief, the total nitrogen was one of the major factors regulating all the bacterioplankton except for Actinobacteria. However, total phosphorus, another important eutrophication factor, contributed to the two largest bacterial groups (Actinobacteria and beta-Proteobacteria), as well as to the Cyanobacteria and Firmicutes. Therefore, the responses of bacterioplankton subgroups to environmental factors were different, and this should be attributed to the differences in the functions of different groups.

Association of dietary type with fecal microbiota in vegetarians and omnivores in Slovenia

The purpose of this study was to discover differences in the human fecal microbiota composition driven by long-term omnivore versus vegan/lacto-vegetarian dietary pattern. In addition, the possible association of demographic characteristics and dietary habits such as consumption of particular foods with the fecal microbiota was examined. This study was conducted on a Slovenian population comprising 31 vegetarian participants (11 lacto-vegetarians and 20 vegans) and 29 omnivore participants. Bacterial DNA was extracted from the frozen fecal samples by Maxwell 16 Tissue DNA Purification Kit (Promega). Relative quantification of selected bacterial groups was performed by real-time PCR. Differences in fecal microbiota composition were evaluated by PCR-DGGE fingerprinting of the V3 16S rRNA region. Participants' demographic characteristics, dietary habits and health status information were collected through a questionnaire. Vegetarian diet was associated with higher ratio (% of group-specific DNA in relation to all bacterial DNA) of Bacteroides-Prevotella, Bacteroides thetaiotaomicron, Clostridium clostridioforme and Faecalibacterium prausnitzii, but with lower ratio (%) of Clostridium cluster XIVa. Real-time PCR also showed a higher concentration and ratio of Enterobacteriaceae (16S rDNA copies/g and %) in female participants (p<0.05 and p<0.01) and decrease in Bifidobacterium with age (p<0.01). DGGE analysis of the 16S rRNA V3 region showed that relative quantity of DGGE bands from certain bacterial groups was lower (Bifidobacterium, Streptococus, Collinsella and Lachnospiraceae) or higher (Subdoligranulum) among vegetarians, indicating the association of dietary type with bacterial community composition. Sequencing of selected DGGE bands revealed the presence of common representatives of fecal microbiota: Bacteroides, Eubacterium, Faecalibacterium, Ruminococcaceae, Bifidobacterium and Lachnospiraceae. Up to 4% of variance in microbial community analyzed by DGGE could be explained by the vegetarian type of diet. Long-term vegetarian diet contributed to quantity and associated bacterial community shifts in fecal microbiota composition. Consumption of foods of animal origin (eggs, red meat, white meat, milk, yoghurt, other dairy products, fish and seafood) and vegetarian type of diet explained the largest share of variance in microbial community structure. Fecal microbiota composition was also associated with participants' age, gender and body mass.

Bioaugmentation of activated sludge with Acinetobacter sp. TW enhances nicotine degradation in a synthetic tobacco wastewater treatment system

Bioaugmentation (BA) using Acinetobacter sp. TW with high nicotine-degrading efficiency was applied in a bioreactor receiving a load of COD (3,200 ± 50 mg/L) and nicotine (1.0 ± 0.1g/L). The results showed that because of the colonization of strain TW, the COD removal was stable at 80-90%, while nicotine removal reached 98% in the BA system. Furthermore, according to PCR-DGGE fingerprinting, compared with the originally activated sludge, more bacteria existed in the BA systems while some bacteria disappeared from the non-BA system. In terms of the quorum sensing, short chain AHLs increased to assist colonization of strain TW, and long chain AHLs were secreted and helped to resist the nicotine toxicity. Compared with the non-BA system, the amounts of ROS, protein carbonyls and 8-OHdG were significant lower in the BA systems, which suggested that strain TW played an important role in eliminating the nicotine toxicity from the bioreactors.

Monitoring the Ecology of Bacillus During Daqu Incubation, a Fermentation Starter, Using Culture-Dependent and Culture-Independent Methods

Daqu, a traditional fermentation starter, has been used to produce attractively flavored foods such as vinegar and Chinese liquor for thousands of years. Although Bacillus spp. are one of the dominant microorganisms in Daqu, more precise information is needed to reveal why and how Bacillus became dominant in Daqu, and next, to assess the impact of Bacillus sp. on Daqu and its derived products. We combined culture-dependent and culture-independent methods to study the ecology of Bacillus during Daqu incubation. Throughout the incubation, 67 presumptive Bacillus spp. isolates were obtained, 52 of which were confirmed by 16S rDNA sequencing. The identified organisms belonged to 8 Bacillus species: B. licheniformis, B. subtilis, B. amyloliquefaciens, B. cereus, B. circulans, B. megaterium, B. pumilus, and B. anthracis. A primer set specific for Bacillus and related genera was used in a selective PCR study, followed by a nested DGGE PCR targeting the V9 region of the 16S rDNA. Species identified from the PCR-DGGE fingerprints were related to B. licheniformis, B. subtilis, B. amyloliquefaciens, B. pumilus, B. benzoevorans, and B. foraminis. The predominant species was found to be B. licheniformis. Certain B. licheniformis strains exhibited potent antimicrobial activities. The greatest species diversity occurred at the Liangmei stage of Daqu incubation. To date, we lack sufficient knowledge of Bacillus distribution in Daqu. Elucidating the ecology of Bacillus during Daqu incubation would enable the impact of Bacillus on Daqu to be accessed, and the quality and stabilization of Daqu-derived products to be optimized.

Response of anaerobes to methyl fluoride, 2-bromoethanesulfonate and hydrogen during acetate degradation

To use the selective inhibition method for quantitative analysis of acetate metabolism in methanogenic systems, the responses of microbial communities and metabolic activities, which were involved in anaerobic degradation of acetate, to the addition of methyl fluoride (CH3F), 2-bromoethanesulfonate (BES) and hydrogen were investigated in a thermophilic batch experiment. Both the methanogenic inhibitors, i.e., CH3F and BES, showed their effectiveness on inhibiting CH4 production, whereas acetate metabolism other than acetoclastic methanogenesis was stimulated by BES, as reflected by the fluctuated acetate concentration. Syntrophic acetate oxidation was thermodynamically blocked by hydrogen (H2), while H2-utilizing reactions as hydrogenotrophic methanogenesis and homoacetogenesis were correspondingly promoted. Results of PCR-DGGE fingerprinting showed that, CH3F did not influence the microbial populations significantly. However, the BES and hydrogen notably altered the bacterial community structures and increased the diversity. BES gradually changed the methanogenic community structure by affecting the existence of different populations to different levels, whilst H2 greatly changed the abundance of different methanogenic populations, and induced growth of new species.

Effects of diphenylarsinic acid on bacterial and archaeal community structures in an anaerobic paddy soil

DPAA is often found as one of the major degradation products in soil and groundwater contaminated with diphenylcyanoarsine or diphenylchloroarsine. These compounds were produced mainly during the World Wars as chemical warfare agents. This study investigated the effect of DPAA contamination on soil bacterial and archaeal community structures under anaerobic conditions in a model experiment using 16S rRNA targeted PCR–DGGE fingerprinting of DNA extracted from the contaminated soil. DPAA decreased in anaerobically incubated soil cultures due to microbiological activity. Addition of rice straw partially enhanced the extent of DPAA degradation. Inorganic arsenic acid, PAA, and an unknown arsenical species were detected as degradation products using LC–ICPMS. PCR–DGGE fingerprinting for bacterial community analysis revealed that anaerobic bacterial and archaeal species, including Clostridium and Methanosarcina, became abundant in the incubated soil within a week. In the soil cultures incubated with DPAA, while a few bacterial bands found on the DGGE gels disappeared or became weaker, most of the bands showed no significant changes. Addition of DPAA had no significant effect on archaeal communities. These findings suggest that, even though DPAA may have a direct effect on some abundant bacterial species, overall bacterial and archaeal community structures under the anaerobic soil conditions tended to be stable regardless of DPAA contamination.

Characterization of Freshwater Diatom Communities: Comparing Taxonomic and Genetic-Fingerprinting Approaches.

Benthic diatom assemblages from five sampling sites located on two rivers were characterized simultaneously by means of traditional microscopic observations and PCR-DGGE fingerprinting with primers specifically designed for Bacillariophyceae. Community structure, richness, and diversity assessed by both methods were compared. Diatom lists obtained from morphological identification were separated into subsets, depending on (i) the taxonomic level considered (genus, species, variety) and, for each of them, (ii) the relative abundance (RA) of each component (the whole data set, RA > 1%, RA>2%). These data were then compared to genetic fingerprinting data. Clusters based on taxonomic composition and DGGE banding patterns were very similar, showing good correspondence of community structure between the two methods. Data were compared by linear regressions between indices (richness, diversity) and by Mantel tests on dissimilarity matrices generated for each community composition data set. Statistical analysis indicated that the most reliable correlations with fingerprinting were obtained for genera representing more than 1% RA or species representing more than 2% RA. The results reveal that the PCR-DGGE protocol described here offers a satisfactory alternative for performing preliminary screening of coarse differences in diatom global community structure between samples. It can be regarded as a good complement to taxonomic analyses, which still remain necessary to detect precise changes in richness and diversity, especially when considering species with low abundance in natural assemblages.

Sequencing Analysis of HA-A/A-MCO Process

This study applies PCR-DGGE fingerprinting technique to analysis the bacterial community structure of phosphorous removal and denitrification system. Through strains identification, it is found that acinetobacter sp.is the base of keeping favorable phosphorus removal effect, Spirochaeta sp.undertakes the function of organic matters removal, Bacillus sp. and Lampropedia hyalina sp.can propagate largely in the germiculture area(No.1 oxic tank), and can be preyed on by highlevel microbe(such as protozoa and metazoan) in protozoa growing area(No.2oxic tank) and metazoan growimg area(No.3 oxic tank). The predation between highlevel microbe and low grade microbe can promote efficient sludge reduction of HA-A/A-MCO process.

Analysis and comparison of bacterial communities in two types of ‘wheatQu’, the starter culture of Shaoxing rice wine, using nested PCR-DGGE

Shaoxing rice wine, manufactured in Shaoxing region of Zhejiang Province, is the best-known Chinese rice wine. In the current study, the bacterial communities associated with two types of ‘wheat Qu’, the Shaoxing rice wine starter cultures, were identified and compared using nested PCR–denaturing gradient gel electrophoresis analysis. DNA sequencing of the highly variable V3 or V9 regions of the 16S rRNA genes obtained from PCR–DGGE fingerprints identified common species related to Saccharopolyspora hordei, S. rectivirgula, Bacillus subtilis, B. amyloliquefaciens and so on. Some sequences associated with a particular type were also identified. For example, Clavibacter michiganensis and Saccharopolyspora sp. were found in the machine- but not in the human-made type, while Curtobacterium plantarum, Thermoactinomyces intermedius, T. vulqaris, B. licheniformis and Bacillus sp. were found in human- but not in machine-made type of wheat Qu. The information gathered from the present research enriches the present knowledge of Shaoxing rice wine-related bacteria, and will also facilitate the long-term objective of selecting bacterial combinations to be used as starter cultures that will more tightly regulate the fermentation process, as well as improve the quality and safety of wheat Qu. Copyright © 2012 The Institute of Brewing & Distilling

Microbial diversity of traditional fermentation starters for Hong Qu glutinous rice wine as determined by PCR-mediated DGGE

Hong Qu glutinous rice wine, one of the most popular traditional rice wines in China, is brewed from glutinous rice with the addition of two traditional fermentation starters – Hong Qu (hóng qū) and Yao Qu (yào qū). In this study, the microbial compositions of fungi and bacteria associated with these two fermentation starters were investigated by nested PCR-denaturing gradient gel electrophoresis (DGGE).The bacterial DGGE profile targeting the V3 region of the 16S rRNA gene indicated that the bacterial composition of starters was highly variable in species composition and dominated by Bacillus species, including Bacillus ginsengihumi, Bacillus megaterium or Bacillus aryabhattai, Bacillus subtilis, Bacillus methylotrophicus and Bacillus amyloliquefaciens. Lactic acid bacteria (LAB) including Weissella paramesenteroides, Pediococcus pentosaceus and Pediococcus acidilactici were also detected in some fermentation starters. In analysis of fungi, PCR-DGGE fingerprints revealed that Rhizopus oryzae, Rhizopus microsporus and Aspergillus sp. were the most frequent species in Yao Qu, while Monascus sp. dominated in Hong Qu. Three non-Saccharomyces yeasts (Saccharomycopsis fibuligera, Pichia guilliermondii and Pichia farinose) were also detected in some starter samples. Multivariate comparisons of DGGE fingerprints showed the complex bacterial and fungal communities were different between Hong Qu and Yao Qu. The Shannon–Weaver diversity index (H′) and Simpson dominance index (D), calculated from the DGGE profiles also showed considerable qualitative differences in the community structure between Hong Qu and Yao Qu.PCR-DGGE was found to be useful for evaluating the quality and the type of traditional wine starters. The prevalence of potential spoilage microorganism highlights the need for more attention when evaluating the microbiological safety of naturally fermented, traditional food products. Moreover, the above results are relevant for the development of starter cultures and predictability of fermentation process for traditional Hong Qu glutinous rice wine, and to aid their intermediate and large scale production.

How water-level drawdown modifies litter-decomposing fungal and actinobacterial communities in boreal peatlands

Microbes decompose fresh organic carbon inputs, such as plant litter, to CO2. Due to a high water-level (WL) in pristine peatlands the decomposition process is retarded and therefore, northern peatlands contain about 30% of the global soil carbon (C) pool. Global warming will decrease the WL of these soil C hotspots and therefore, the responses of the decomposition process of plant litter to shifts in WL regime is of interest. Two important decomposer communities, fungi and actinobacteria, were studied in a diverse set of litters incubated over two years in a boreal peatland. The experimental design involved a non-treatment control and plots experiencing short-term (ca 4 yrs) and long-term (ca 40 yrs) WL drawdown. The responses of litter-inhabiting fungal and actinobacterial decomposers to environmental variables (WL regime, site type, litter quality) were evaluated using PCR-DGGE fingerprinting and direct sequencing of regions within the 16S and 18S ribosomal RNA genes after reverse transcription of RNA into its complementary DNA.The fungal sequences found in the decomposing litters represented organisms from a variety of fungal taxa, whereas most of the actinobacterial sequences were only distantly similar to known actinobacteria. Our results indicated that: (1) WL regime and site type had minor impacts on the litter-inhabiting microbial community composition, (2) litter quality had the strongest impact on the communities, especially on fungi; (3) decomposition stage had an impact on the fungal community composition, showing a possible change from mycorrhizal to saprotrophic fungi and (4) mass loss of the litters after the two-year-decomposition period was not related to the variation in fungal community composition and only to a negligible extent to the actinobacterial community composition. In relation to the decomposition process these results align with the idea of functional redundancy in microbial communities, which does not seem to be modified by moderate WL drawdown. Overall, our results indicate that the WL regime modifies the litter-inhabiting microbial communities largely indirectly via litter quality.

Variation in microbial responses and Rhizoctonia solani AG2-2IIIB growth in soil under different organic amendment regimes

Organic amendments influence chemical and microbial compositions in soils and also susceptibility to plant diseases. The purpose of this study was to establish different parameters that interfere with pathogen growth in soil. Four different organic-amendment regimes, i.e. slurry, compost, slurry-dung and compost-slurry-dung, were applied to two fields proximate to each other on the same farm and covered with the same grass-clover ley in the last two years preceding sampling. Before that period, there were differences in cropping and management practices between both fields. Chemical analyses of the soils revealed no differences between organic amendments, whereas significant differences were present between fields in all C, N and pH values. Growth of R. solani AG2-2IIIB in soil, measured by damping-off in sugar beet plants, was influenced by the interaction of organic amendment with field type. Diversity and evenness values of the microbial communities, studied by PCR-DGGEs specific for bacteria, fungi, Pseudomonas and ammonia-oxidizing β-proteobacteria, revealed different patterns, i.e. no differences between organic amendments, but clear differences between fields. Multivariate analyses done on individual species of the four groups, as represented by band location and size in PCR-DGGE fingerprints, and by inclusion of chemical and R. solani AG2-2IIIB growth parameters as ‘environmental’ variables, revealed strong and occasionally significant effects of organic matter content, water-dissolvable organic carbon and pH on microbial communities. It was therefore concluded that different organic amendments had different effects on pathogen growth in soils of both fields and that organic matter content and pH influenced soil microbial compositions most.

Applicability of PCR-DGGE and 16S rDNA Sequencing for Microbiological Analysis of Otitis Media with Effusion

Background: The aim of the study was to analyze the performance of PCR-DGGE based assay and its applicability as a tool for the identification of bacteria in the middle ear of children with otitis media with effusion (OME). Methods: The middle ear effusions from 20 children with OME were analyzed both by bacterial culture and by 16S rDNA-gene-targeted PCR assay, DGGE fingerprinting and sequencing analysis. Results: In bacterial culture assay, only three middle ear effusions (15%) showed bacterial growth. None of the samples were positive for anaerobic culture. The PCR assay with 16S rDNA-gene-targeted universal primers was positive in 10 (50%) cases. The subsequent DGGE fingerprinting and 16S rDNA sequencing analysis revealed that the most commonly encountered bacteria in the middle ear effusions of children with OME are Haemophilus influenzae, Alloiococcus otitidis and Bacteroides spp. Conclusions: The present study demonstrated the applicability of PCR-DGGE based assay and 16S rDNA sequencing for analyzing of bacterial diversity in the middle ear effusion of children OME. The results of our study may contribute to a better understanding of the etiology of OME.

Changes in Human Fecal Microbiota Due to Chemotherapy Analyzed by TaqMan-PCR, 454 Sequencing and PCR-DGGE Fingerprinting

BackgroundWe investigated whether chemotherapy with the presence or absence of antibiotics against different kinds of cancer changed the gastrointestinal microbiota.Methodology/Principal FindingsFeces of 17 ambulant patients receiving chemotherapy with or without concomitant antibiotics were analyzed before and after the chemotherapy cycle at four time points in comparison to 17 gender-, age- and lifestyle-matched healthy controls. We targeted 16S rRNA genes of all bacteria, Bacteroides, bifidobacteria, Clostridium cluster IV and XIVa as well as C. difficile with TaqMan qPCR, denaturing gradient gel electrophoresis (DGGE) fingerprinting and high-throughput sequencing. After a significant drop in the abundance of microbiota (p = 0.037) following a single treatment the microbiota recovered within a few days. The chemotherapeutical treatment marginally affected the Bacteroides while the Clostridium cluster IV and XIVa were significantly more sensitive to chemotherapy and antibiotic treatment. DGGE fingerprinting showed decreased diversity of Clostridium cluster IV and XIVa in response to chemotherapy with cluster IV diversity being particularly affected by antibiotics. The occurrence of C. difficile in three out of seventeen subjects was accompanied by a decrease in the genera Bifidobacterium, Lactobacillus, Veillonella and Faecalibacterium prausnitzii. Enterococcus faecium increased following chemotherapy.Conclusions/SignificanceDespite high individual variations, these results suggest that the observed changes in the human gut microbiota may favor colonization with C.difficile and Enterococcus faecium. Perturbed microbiota may be a target for specific mitigation with safe pre- and probiotics.

Bacterial communities associated with a mineral weathering profile at a sulphidic mine tailings dump in arid Western Australia

We investigated bacterial community assemblages and functions down a hill slope contaminated by tailings from a volcanogenic massive sulphide mine in arid Western Australia. Weathering of waste rock, high in S and Fe, had resulted in a varying elemental dispersal down a face of the tailings hill. Bacterial community assemblage, characterised by PCR-DGGE fingerprinting, was significantly associated with electrical conductivity (E.C.) (ρ = 0.664; P < 0.01). Analysis of mobile salts showed that E.C. values were driven by ionic S, Zn, Cl and Al. The bacterial community assemblage was directly characterised across an E.C. gradient using an oligonucleotide microarray (PhyloChip). The dominant taxa at the site were Proteobacteria, Actinobacteria and Firmicutes; however, 37 phyla were detected. The most responsive taxa to variation in E.C. was Acidobacteria (negative correlation). Patterns of heterotrophic processes (BioLog analysis) were also best explained by variation in E.C. (ρ = 0.53; P < 0.01), showing a link between primary mineral weathering by lithotrophic bacteria and abiotic processes, and secondary biogeochemical processes by heterotrophic taxa. These data significantly broaden our knowledge of the bacteria present in metallomorphic ecosystems, establish that mobile phase elements are key drivers of community structure, and that primary biogeochemical cycling is directly influencing other geochemical interactions in the samples.

Assessing microbiological surface expression over an overburden-covered VMS deposit

An integrated biogeochemical sampling approach, consisting of soil geochemistry, plant biogeochemical analyses and investigation of microbial community structure and function, was used to characterize a surficial geochemical signature of the buried Jaguar volcanogenic massive sulfide (VMS) Ag-Cu-Zn deposit in Western Australia's NE goldfields region. The study is a proof of concept in using multiple science disciplines (microbiology, geochemistry, regolith) to evaluate surface anomalies related to exploration. In a factorial design, soil from the surface (1–5 cm) and sub-surface (10–20 cm) horizons, was sampled under trees in locations directly adjacent to the stem base and also further under the canopy. Samples of mulga foliage and litter resting on the soil were sampled. Soil and plant material were collected from trees above the projected zone of mineralization and from background areas. Significant differences ( P < 0.05) in elemental composition of soil, foliage and litter collected from between mineralized and background samples exist. The soil anomaly exhibited elevated concentrations of Cu and Zn, which were concentrated in the top soil horizon. Concentrations of Ag, Sr, Hg, Na and Ca were also significantly higher in soil sampled over the mineralization. Mulga foliage (phyllodes), and particularly fallen mulga litter, had elevated concentrations of Cu and Zn ( P < 0.05) over the mineralization. Microbial processes involved in organic matter cycling (litter decomposition) under the mulga were investigated using BioLog EcoPlates. Compared to background samples, the patterns of substrate utilization were significantly different in soil ( P < 0.05) collected from under plants growing above the mineralization, however the rates of microbial processes were higher in soil adjacent to the base of the plant stems. Utilization of the carbohydrates glucose-1-phosphate, β-methyl- d-glucose, and α- d-lactose were significantly increased in the mineralized soils, whereas the utilization of various carboxylic acids, polymers, phenolic and amine compounds were suppressed. The genetic structure of the soil bacterial, archaeal and fungal communities, determined using PCR-DGGE fingerprinting of rRNA genes, were also significantly different above the buried mineralization. Changes in the bacterial community were most pronounced, and were associated with Gemmatimonadaceae, Acidobacteriaceae, Oxalobacteraceae, Bradyrhizobiaceae, Caulobacteraceae, TM7 genera incertae sedis, and unclassified bacteria. Thus, the biogeochemical anomaly associated with the buried mineralization is also expressed in soil microbial communities. We propose that the formation of the surficial soil anomaly is a product of plant concentration of elements via scavenging from the surrounding regolith profile followed by the microbially-mediated release of metals to the soil surface following plant litter fall. The methods employed and the discovery of anomalous microbial processes and communities has implications for mineral exploration. Future investigations using these techniques will provide mechanistic support to models describing the formation of biogeochemical anomalies in general. Results have also shown that biogeochemical approaches to mineral exploration are viable in arid ecosystems with low net primary productivity.

Analysis of the fungal, archaeal and bacteriophage diversity in the human distal gut

The composition and role of bacteria in the human gut has been studied intensely and is a burgeoning field of scientific research. However, there is a relative lack of research on other microorganisms which compose our gut flora such as bacteriophage, archaea and fungi. The aim of our study was to begin to fill this gap. The archaeal, fungal and bacteriophage diversity in the gut was analyzed using a PCR-DGGE fingerprinting method on fecal samples from 3 healthy donors. These samples were inoculated into chemostats and the microbes were grown in continuous culture to model the interactions of our flora in vitro. Norepinephrine was also added to the chemostats to test the microbial community’s reaction to stress. Here we report that, relative to bacteria, fungal and archaeal diversity in the gut is low. The archaeal populations seemed stable over time varied depending on the individual. Fungal populations were more variable over time and changes in the community structure were observed after the addition of norepinephrine. DNA sequence analysis confirmed the presence of fungal species that are not yet cultured, yet are residents of the gut. Species of Podophage can also be detected as residents of the gut based on sequence analysis. It is clear that there is a core set of archaeal and fungal species living as residents in the gut. Bacteriophage are also present but their ecological role and effect on the microbial community in the gut is unknown.

Analysis of bacterial communities of traditional fermented West African cereal foods using culture independent methods

In this study, the microbial composition of kunu-zaki and ogi, two popular foods in Nigeria produced after natural, uncontrolled fermentation of cereals, was assessed by culture-independent molecular profiling methods. In particular, PCR–denaturing gradient gel electrophoresis and construction of 16S rRNA gene clone libraries revealed the presence of diverse bacterial communities. DNA sequencing of the highly variable V3 region of the 16S rRNA genes obtained from PCR–DGGE fingerprints identified species related to Weissella confusa, Lactobacillus fermentum, Lactobacillus amylolyticus, Lactobacillus delbrueckii subsp. bulgaricus, Bacillus spp. and Lactococcus lactis spp lactis from food samples obtained from northern and southern geographical locations. A more comprehensive analysis of 272 full-length 16S rRNA gene inserts revealed that 70% of them were assigned to the Lactobacillaceae family and 19% to the Streptococcaceae family. Interestingly, sequences associated with a particular food type were also identified. For example, L. plantarum, L. pantheris and L. vaccinostercus were found in ogi but not in kunu-zaki while W. confusa, Streptococcus lutetiensis and Streptococcus gallolyticus subsp. macedonicus were found in kunu-zaki but not in ogi. Phylotypes corresponding to potentially pathogenic bacteria, such as Clostridium perfringens and Bacillus cereus were also detected highlighting the need for controlled fermentation processes.