Bacterial Population Dynamics Research Articles

Assessing the Unseen Bacterial Diversity in Microbial Communities.

For both historical and technical reasons, 16S ribosomal RNA has been the most common molecular marker used to analyze the contents of microbial communities. However, its slow rate of evolution hinders the resolution of closely related bacteria—individual 16S-phylotypes, particularly when clustered at 97% sequence identity, conceal vast amounts of species- and strain-level variation. Protein-coding genes, which evolve more quickly, are useful for differentiating among more recently diverged lineages, but their application is complicated by difficulties in designing low-redundancy primers that amplify homologous regions from distantly related taxa. Given the now-common practice of multiplexing hundreds of samples, adopting new genes usually entails the synthesis of large sets of barcoded primers. To circumvent problems associated with use of protein-coding genes to survey microbial communities, we develop an approach—termed phyloTAGs—that offers an automatic solution for primer design and can be easily adapted to target different taxonomic groups and/or different protein-coding regions. We applied this method to analyze diversity within the gorilla gut microbiome and recovered hundreds of strains that went undetected after deep-sequencing of 16S rDNA amplicons. PhyloTAGs provides a powerful way to recover the fine-level diversity within microbial communities and to study stability and dynamics of bacterial populations.

Elucidation of rice rhizosphere metagenome in relation to methane and nitrogen metabolism under elevated carbon dioxide and temperature using whole genome metagenomic approach

Carbon (C) and nitrogen (N) mineralization is one of the key processes of biogeochemical cycling in terrestrial ecosystem in general and rice ecology in particular. Rice rhizosphere is a rich niche of microbial diversity influenced by change in atmospheric temperature and concentration of carbon dioxide (CO2). Structural changes in microbial communities in rhizosphere influence the nutrient cycling. In the present study, the bacterial diversity and population dynamics were studied under ambient CO2 (a-CO2) and elevated CO2+temperature (e-CO2T) in lowland rice rhizosphere using whole genome metagenomic approach. The whole genome metagenomic sequence data of lowland rice exhibited the dominance of bacterial communities including Proteobacteria, Firmicutes, Acidobacteria, Actinobacteria and Planctomycetes. Interestingly, four genera related to methane production namely, Methanobacterium, Methanosphaera, Methanothermus and Methanothermococcus were absent in a-CO2 but noticed under e-CO2T. The acetoclastic pathway was found as the predominant pathway for methanogenesis, whereas, the serine pathway was found as the principal metabolic pathway for CH4 oxidation in lowland rice. The abundances of reads of enzymes in the acetoclastic methanogenesis pathway and serine pathways of methanotrophy were much higher in e-CO2T (328 and 182, respectively) as compared with a-CO2 (118 and 98, respectively). Rice rhizosphere showed higher structural diversities and functional activities in relation to N metabolism involving nitrogen fixation, assimilatory and dissimilatory nitrate reduction and denitrification under e-CO2T than that of a-CO2. Among the three pathways of N metabolism, dissimilarity pathways were predominant in lowland rice rhizosphere and more so under e-CO2T. Consequently, under e-CO2T, CH4 emission, microbial biomass nitrogen (MBN) and dehydrogenase activities were 45%, 20% and 35% higher than a-CO2, respectively. Holistically, a high bacterial diversity and abundances of C and N decomposing bacteria in lowland rice rhizosphere were found under e-CO2T, which could be explored further for their specific role in nutrient cycling, sustainable agriculture and environment management.

Interlinkages between bacterial populations dynamics and the operational parameters in a moving bed membrane bioreactor treating urban sewage

Bacteria are key players in biological wastewater treatments (WWTs), thus a firm knowledge of the bacterial population dynamics is crucial to understand environmental/operational factors affecting the efficiency and stability of the biological depuration process. Unfortunately, little is known about the microbial ecology of the advanced biological WWTs combining suspended biomass (SB) and attached biofilms (AB). This study explored in depth the bacterial community structure and population dynamics in each biomass fraction from a pilot-scale moving bed membrane bioreactor (MBMBR) treating municipal sewage, by means of temperature-gradient gel electrophoresis (TGGE) and 454-pyrosequencing. Eight experimental phases were conducted, combining different carrier filling ratios, hydraulic retention times and concentrations of mixed liquor total suspended solids. The bacterial community, dominated by Proteobacteria (20.9–53.8%) and Actinobacteria (20.6–57.6%), was very similar in both biomass fractions and able to maintain its functional stability under all the operating conditions, ensuring a successful and steady depuration process. Multivariate statistical analysis demonstrated that solids concentration, carrier filling ratio, temperature and organic matter concentration in the influent were the significant factors explaining population dynamics. Bacterial diversity increased as carrier filling ratio increased (from 20% to 35%, v/v), and solids concentration was the main factor triggering the shifts of the community structure. These findings provide new insights on the influence of operational parameters on the biology of the innovative MBMBRs.

Dynamic control and quantification of bacterial population dynamics in droplets

Culturing and measuring bacterial population dynamics are critical to develop insights into gene regulation or bacterial physiology. Traditional methods, based on bulk culture to obtain such quantification, have the limitations of higher cost/volume of reagents, non-amendable to small size of population and more laborious manipulation. To this end, droplet-based microfluidics represents a promising alternative that is cost-effective and high-throughput. However, difficulties in manipulating the droplet environment and monitoring encapsulated bacterial population for long-term experiments limit its utilization. To overcome these limitations, we used an electrode-free injection technology to modulate the chemical environment in droplets. This ability is critical for precise control of bacterial dynamics in droplets. Moreover, we developed a trapping device for long-term monitoring of population dynamics in individual droplets for at least 240 h. We demonstrated the utility of this new microfluidic system by quantifying population dynamics of natural and engineered bacteria. Our approach can further improve the analysis for systems and synthetic biology in terms of manipulability and high temporal resolution.

The differential effects of ammonium and nitrate on methanotrophs in rice field soil

It has been known that nitrogenous fertilizers can either stimulate or inhibit methane oxidation in soils. The mechanism, however, remains unclear. Here we conducted laboratory incubation experiments to evaluate the effects of ammonium versus nitrate amendment on CH4 oxidation in a rice field soil. The results showed that both N forms stimulated CH4 oxidation. But nitrate stimulated CH4 oxidation to a greater extent than ammonium per unit N base. The 16S rRNA genes and the pmoA genes were analyzed to determine the dynamics of total bacterial and methanotrophic populations, respectively. The methanotrophic community consisted of type I and type II methanotrophs and was dominated by type I group after two weeks of incubation. Nitrate promoted both types of methanotrophs, but ammonium promoted only type I. DNA-based stable isotope probing confirmed that ammonium stimulated the incorporation of 13CH4 into type I methanotrophs but not type II, while nitrate caused almost homogenous distribution of 13CH4 in type I and type II methanotrophs. Our study suggests that nitrate can promote CH4 oxidation more significantly than ammonium and is probably a better N source for both types of methanotrophs in rice field soil. More investigations, e.g. using 15N labeling, are necessary to elucidate this possibility.

English

A study was carried out in a screen house to determine the bacterial population dynamics in a crude oil soil undergoing bioremediation. The agricultural soil samples were polluted with different concentrations (5, 8 and 11%) of crude oil. Physiochemical and microbiological analyses were carried out on the polluted and unpolluted soil samples at various intervals beginning from two weeks after the pollution of the soil samples to the fourteenth week. The soil samples were found to be acidic (5.40) and rich in phosphorous (26.52 mg/kg). There were no significant differences in the pH, organic matter, sodium, potassium and magnesium of the unpolluted and the polluted soil samples. The microbial loads of the polluted soil samples were lower than the unpolluted soil samples throughout the study. The highest bacterial loads (27.00d±2.20, 19.40c±1.80, 8.70b±0.50 for 5, 8 and 11% crude oil concentration respectively) were observed, when Ewingella americana (bacterium with known crude oil degrading ability) was inoculated into the polluted soil samples. The bacterial species responsible for the bioremediation from the polluted soil samples were identified using conventional techniques. The bacterial species isolated and identified were Pseudomonas aeruginosa, Bacillus subtilis, Bacillus cereus, Proteus vulgaris and Staphylococcus aureus. Bacillus spp has the highest percentage frequency (Bacillus subtilis = 30.95% and Bacillus cereus = 21.43%). The consistent isolation of these bacteria shows that they could survive the crude oil pollution and possibly utilize the crude oil, thereby making the crude oil less harmful to the environment. Key words: Bacteria, bioremediation, bacterial species, crude oil.

Effect of sublethal preculturing on the survival of probiotics and metabolite formation in set-yoghurt

The objective of this study was to investigate the effect of preculturing of Lactobacillus rhamnosus GG and Bifidobacterium animalis subsp. lactis BB12 under sublethal stress conditions on their survival and metabolite formation in set-yoghurt. Prior to co-cultivation with yoghurt starters in milk, the two probiotic strains were precultured under sublethal stress conditions (combinations of elevated NaCl and low pH) in a batch fermentor. The activity of sublethally precultured probiotics was evaluated during fermentation and refrigerated storage by monitoring bacterial population dynamics, milk acidification and changes in volatile and non-volatile metabolite profiles of set-yoghurt. The results demonstrated adaptive stress responses of the two probiotic strains resulting in their viability improvement without adverse influence on milk acidification. A complementary metabolomic approach using SPME-GC/MS and 1H-NMR resulted in the identification of 35 volatiles and 43 non-volatile polar metabolites, respectively. Principal component analysis revealed substantial impact of the activity of sublethally precultured probiotics on metabolite formation demonstrated by distinctive volatile and non-volatile metabolite profiles of set-yoghurt. Changes in relative abundance of various aroma compounds suggest that incorporation of stress-adapted probiotics considerably influences the organoleptic quality of product. This study provides new information on the application of stress-adapted probiotics in an actual food-carrier environment.

Bacterial communities along stratified water columns at the Chukchi Borderland in the western Arctic Ocean

An expedition of the IBRV ARAON took place in the Arctic Ocean during the summer of 2010. To investigate the hydrographic features and bacterial variations in water columns, we categorized 16 water samples collected from distinct water masses at the Chukchi Borderland in the western Arctic Ocean. Bacterial diversity, relative abundance, and community composition were determined based on a pyrosequencing approach, and their relationship with water mass properties was considered. Alphaproteobacteria (43.2%), Gammaproteobacteria (16.7%), Flavobacteria (13.7%), and Deltaproteobacteria (12.0%) were the most common bacteria found in all samples, and the relative abundance of these predominant taxa represent the population dynamics of bacterial communities in different water masses (from the euphotic to the sub-euphotic zone) in the Arctic Ocean. Furthermore, the relative abundance of Alphaproteobacteria and its subgroup, SAR11 group I, were significantly related to depth change in water columns, suggesting that environmental heterogeneity caused by changes in depth may play an important role in bacterial population dynamics. In this study, bacterial communities in the Arctic Ocean exhibit biogeographic patterns according to the type of water mass. The halocline layer between the Pacific winter water and Atlantic water exhibits a variation in the composition of bacterial communities, which may be influenced by mixing of Pacific winter water and Atlantic water.

Dissemination of a highly virulent pathogen: tracking the early events that define infection.

The series of events that occurs immediately after pathogen entrance into the body is largely speculative. Key aspects of these events are pathogen dissemination and pathogen interactions with the immune response as the invader moves into deeper tissues. We sought to define major events that occur early during infection of a highly virulent pathogen. To this end, we tracked early dissemination of Yersinia pestis, a highly pathogenic bacterium that causes bubonic plague in mammals. Specifically, we addressed two fundamental questions: (1) do the bacteria encounter barriers in disseminating to draining lymph nodes (LN), and (2) what mechanism does this nonmotile bacterium use to reach the LN compartment, as the prevailing model predicts trafficking in association with host cells. Infection was followed through microscopy imaging in addition to assessing bacterial population dynamics during dissemination from the skin. We found and characterized an unexpected bottleneck that severely restricts bacterial dissemination to LNs. The bacteria that do not pass through this bottleneck are confined to the skin, where large numbers of neutrophils arrive and efficiently control bacterial proliferation. Notably, bottleneck formation is route dependent, as it is abrogated after subcutaneous inoculation. Using a combination of approaches, including microscopy imaging, we tested the prevailing model of bacterial dissemination from the skin into LNs and found no evidence of involvement of migrating phagocytes in dissemination. Thus, early stages of infection are defined by a bottleneck that restricts bacterial dissemination and by neutrophil-dependent control of bacterial proliferation in the skin. Furthermore, and as opposed to current models, our data indicate an intracellular stage is not required by Y. pestis to disseminate from the skin to draining LNs. Because our findings address events that occur during early encounters of pathogen with the immune response, this work can inform efforts to prevent or control infection.

The influence of light and water mass on bacterial population dynamics in the Amundsen Sea Polynya

Abstract Despite being perpetually cold, seasonally ice-covered and dark, the coastal Southern Ocean is highly productive and harbors a diverse microbiota. During the austral summer, ice-free coastal patches (or polynyas) form, exposing pelagic organisms to sunlight, triggering intense phytoplankton blooms. This strong seasonality is likely to influence bacterioplankton community composition (BCC). For the most part, we do not fully understand the environmental drivers controlling high-latitude BCC and the biogeochemical cycles they mediate. In this study, the Amundsen Sea Polynya was used as a model system to investigate important environmental factors that shape the coastal Southern Ocean microbiota. Population dynamics in terms of occurrence and activity of abundant taxa was studied in both environmental samples and microcosm experiments by using 454 pyrosequencing of 16S rRNA genes. We found that the BCC in the photic epipelagic zone had low richness, with dominant bacterial populations being related to taxa known to benefit from high organic carbon and nutrient loads (copiotrophs). In contrast, the BCC in deeper mesopelagic water masses had higher richness, featuring taxa known to benefit from low organic carbon and nutrient loads (oligotrophs). Incubation experiments indicated that direct impacts of light and competition for organic nutrients are two important factors shaping BCC in the Amundsen Sea Polynya.

Dynamics and Activity of Sulfate-Reducing Bacterial Populations in Paddy Soil under Subsurface Drainage: Case Study of Kamboinse in Burkina Faso

Sulfide toxicity is a common disease generally associated with iron toxicity which occurs in rice fields when the Sulfate-Reducing Bacteria (SRB) produce sulfides ions in anaerobic conditions. The high quantity of sulfides ions in the soil solution upsets the mineral element balance in the rice, affects its growth and causes crop yield losses. In Burkina Faso, many rice field soils are abandoned due to sulfides toxicity. The present study was developed to evaluate the impact of subsurface drainage on SRB dynamics and activity during rice cultivation and the incidence on rice production. Twelve concrete microplots with a clay-loam soil and a rice variety susceptible to sulfides toxicity (FKR 19) were used for the experiment. Soil in microplots was drained for 7 days (P1), 14 days (P2), and 21 days (P3), respectively. Control (T) microplots without drainage were prepared similarly. The evolution of SRB populations and the content of sulfides ions in the paddy soil and in soil near rice roots were monitored throughout the cultural cycle using MPN and colorimetric methods, respectively. Data obtained were analyzed in relation to drainage frequency, rice growth stage, and rice yield using the Student’s t-test and XLSTAT 7.5.2 statistical software. From the results obtained, the subsurface drainage did not affect significantly SRB populations (P = 0.187). However, the drainage affected significantly sulfides concentration in the soil near rice roots (P = 0.032). The concentration of sulfides (P < 0.0001) in soil near rice roots and the number of SRB (P < 0.0001) were significantly higher during the rice tillering and maturity stages. Although no significant difference was observed for rice yield among treatments (P = 0.209), the P2 subsurface drainage showed the highest yield and a low concentration of sulfides in soil near rice roots.

Dynamics and Activity of Iron-Reducing Bacterial Populations in a West African Rice Paddy Soil under Subsurface Drainage: Case Study of Kamboinse in Burkina Faso

Iron toxicity is one of the main edaphic constraints that hamper rice production in West African savanna and forest lowlands. Although chemical reduction processes of various types of pedogenic iron oxides could not be underestimated, the bulk of these processes can be ascribed to the specific activity of Iron-Reducing Bacteria (IRB). The reducing conditions of waterlogged lowland soils boost iron toxicity through the reduction of almost all iron into ferrous form (Fe2+), which can cause disorder in rice plant and crop yield losses. Aiming to contribute at the improvement of rice yield in Africa, an experiment was developed to evaluate the impact of subsurface drainage on IRB dynamics and activity during rice cultivation. Twelve concrete microplots with a clay-loam soil and a rice variety susceptible to iron toxicity (FKR 19) were used for the experiment. Soil in microplots was drained for 7 days (P1), 14 days (P2), and 21 days (P3), respectively. Control (T) microplots without drainage were prepared similarly. The evolution of IRB populations and the content of ferrous iron in the paddy soil and in soil near rice root were monitored throughout the cultural cycle using MPN and colorimetric methods, respectively. Data obtained were analyzed in relation to drainage frequency, rice growth stage, and rice yield using the Student t test and XLSTAT 7.5.2 statistical software. From the results obtained, the subsurface drainage reduced significantly IRB populations (p = 0.024). However, the drainage did not affect significantly ferrous iron concentration in the soil near rice roots (p = 0.708). The concentration of ferrous iron (p < 0.0001) in soil near rice roots and the number of IRB (p < 0.0001) were significantly higher during the rice tillering and maturity stages. Although no significant difference was observed for rice yield among treatments (p = 0.209), the P2 subsurface drainage showed the highest yield and the lowest concentration of ferrous iron in soil near rice roots.

Isolation and Identification of Rhizospheric Bacteria in Sugarcane (Saccharum spp. L.) Cultivated on Acrisols and Ferrasols of Dong Nai Province, the Southeast of Vietnam

Nitrogen-fixing and phosphate-solubilizing bacterial diversity and population dynamics in the Acrisol and Ferrasol rhizosphere of sugarcane grown in Dong Nai province, the eastern of South Vietnam was studied. Soil rhizosphere samples were taken in three districts (sites) of this region. Physical and chemical characteristics of soil samples and total nitrogen-fixing and phosphate-solubilizing bacteria counts were determined by drop plate count method together with 16S rRNA gene fragments amplified from DNA using eubacterial universal primers (27F and 1492R). A total of 31 isolates were isolated on two media (Burk’s N-free and NBRIP) and all of them have ability of nitrogen fixation and phosphate solubilization together with IAA biosynthesis. Population of nitrogen-fixing and phosphate-solubilizing bacteria correlated with N total concentration and organic matter content in soil closely (P<0.05). The sequences from selected nitrogen-fixing and phosphate-solubilizing bacteria (12 isolates) showed high degrees of similarity to those of the GenBank references strains (between 98% and 99%). From 12 isolates, 7 belonged to Bacilli, while 2 were Beta-Proteobacteria, 1 was Acidobacteria and 2 were Bacteroides. Based on Pi value (nucleotide diversity), Bacilli group had the highest theta value and Theta values (persequence) from S of SNP for DNA polymorphism were calculated for each group and Bacilli group had the highest values in comparison to three groups. From these results showed that two strains (Bacillus megaterium B6 (Ferrasols) and Sphingomonas sp. P14 (Acrisols)) revealed promising candidates with multiple beneficial characteristics and they have the potential for application as inoculants adapted to poor soils and sugarcane tree because they are not only famous strains but also are safety strains for agricultural sustainable.

Treated agro-industrial wastewater irrigation of tomato crop: Effects on qualitative/quantitative characteristics of production and microbiological properties of the soil

A comparative study was carried out to evaluate the effects of two water irrigation sources on the quality and microbiological safety of tomato plants and fruit, and on the microbiological soil properties: irrigation with groundwater (GW) and with treated agro-industrial wastewater (TW). In a field experiment in southern Italy (Apulia region), the physico-chemical characteristics of the irrigation waters and the fruit quality parameters were determined. Escherichia coli, fecal Enterococci and Salmonella spp. were also monitored in the irrigation waters, tomato plant and fruit, and root-zone soil. Bacteriological analysis for total heterotrophic counts (THCs) were determined for plant, fruit, and soil samples. The irrigation water source did not significantly affect yield quantitative traits. However, with GW, the marketable fruit yield was higher than with TW (∼82 vs. ∼79Mgha−1, respectively). For both irrigation treatments, the most important qualitative parameters that characterize the processing tomato fruit (i.e., dry matter content, pH, soluble solid content, color parameters) were in agreement with reports in the literature. For the microbiological results, the mean levels of E. coli and fecal Enterococci were 4408 and 3804CFU 100ml−1, respectively, for TW (above the Italian guidelines for TW re-use). For the tomato plant and fruit, no E. coli isolated in either, and fecal coliforms and THC were not influenced by the irrigation waters (P>0.05). Total bacterial enumeration by quantitative PCR was lower in soil irrigated with GW, than TW (3.69 vs. 4.02, ×106, respectively). Moreover, soil microbial community patterns substantially differed between the two water treatments. These data show that while fecal indicators are not affected, the community composition and dynamics of the whole bacterial population in soil is influenced by the different qualities of these waters used for irrigation.

Characterization of the microbial community structure in ‘Candidatus Liberibacter asiaticus’-infected citrus plants treated with antibiotics

The updated PhyloChipTM G3 were used to explore the differences in the relative abundance and phylogenetic diversity of the bacterial communities associated with HLB-affected citrus plants in the field over a growing season and those treated with antibiotic combinations of AG (Ampicillin at 1000 mg/L and Gentamicin at 100 mg/L) and PS (Penicillin at 1000 mg/L and Streptomycin at 100 mg/L). Both antibiotic treatments resulted in significantly lower Las bacterial titers (Pr&lt;0.05) and their hybridization scores. Of the 50,000+ available operational taxonomic units (OTUs) on PhyloChip™ G3, 7,028 known OTUs in 58 phyla were detected from the field plants, and 7,407 OTUs in 53 phyla from the inoculated potted plants. Proteobacteria was the constantly dominant phylum of bacteria (38.7%~44.1%) vying for prevalence based on the season, followed by Firmicutes (23.5%~29.0%), Actinobacteria (12.4%~16.1%), Bacteroidetes (6.2%~6.6%) and Cyanobacteria (2.3%~3.2%). Circular tree comparing the Las-free and the Las-infected samples indicated that only 17 families present in the Las-free plants, such as Cyanobacteriaceae; but more than 137 families detected in the Las-infected plants, such as Staphylococcaceae and Pseudonocardiaceae. Cyanobacteria are believed to be responsible for introducing oxygen into the atmosphere and fixing nitrogen and phosphorus assimilation for plant growth. Both Staphylococcaceae and Pseudonocardiaceae were recognized as an emerging opportunistic pathogen of plant and animals. When compared to the bacterial populations in the leaves of citrus trees receiving the water control treatment, the Bacteroidete population decreased (Pr&lt;0.05) by 59.6% and 51.8% in the plants receiving AG and PS treatments, respectively. The overall diversity of bacteria also decreased with the antibiotic treatments. Bacterial cells in close proximity may be able to modify their microenvironment; thus, making the composition of the microbial community an important factor in the ability of Las to cause HLB progression. A low Las level was seen as a both a seasonal fluctuation, part of the bacterial population dynamics, and as a response to the antibiotic treatments.

Temperature dependent bacteriophages of a tropical bacterial pathogen.

There is an increasing awareness of the multiple ways that bacteriophages (phages) influence bacterial evolution, population dynamics, physiology, and pathogenicity. By studying a novel group of phages infecting a soil borne pathogen, we revealed a paradigm shifting observation that the phages switch their lifestyle according to temperature. We sampled soil from an endemic area of the serious tropical pathogen Burkholderia pseudomallei, and established that podoviruses infecting the pathogen are frequently present in soil, and many of them are naturally occurring variants of a common virus type. Experiments on one phage in the related model B. thailandensis demonstrated that temperature defines the outcome of phage-bacteria interactions. At higher temperatures (37°C), the phage predominantly goes through a lytic cycle, but at lower temperatures (25°C), the phage remains temperate. This is the first report of a naturally occurring phage that follows a lytic or temperate lifestyle according to temperature. These observations fundamentally alter the accepted views on the abundance, population biology and virulence of B. pseudomallei. Furthermore, when taken together with previous studies, our findings suggest that the phenomenon of temperature dependency in phages is widespread. Such phages are likely to have a profound effect on bacterial biology, and on our ability to culture and correctly enumerate viable bacteria.

Effect of Stimulants on Biogenic Methane Formation and Dynamics of Bacterial Population

Coal bed methane (CBM) is a renewable energy source produced through thermogenic and biogenic activity during the coal formation process. The aim of this research was to stimulate biogenic methane formation using simple carbon as stimulant. The microcosm set-up was done using subbituminous coal at 37°C in an anaerobic chamber. Stimulation with Na-acetate, methanol, formic acid, and no additions, respectively, was carried out for 54 days; observation took place on day 2, 15, 24, 45, and54. The results of all treatments showed differences in the initial pH of the basal medium: 7.76 (Na-acetate), 6.69 (methanol), 4.06 (formic acid), and 8.95 (no stimultant), respectively. Addition of Na-acetate resulted in the highest methane formation rate (5.034 mmol/g coal on day 24 of incubation), followed by methanol (4.377 mmol/g on day 24 of incubation), formic acid (2.520 mmol/g on day 22 of incubation), and no addition (1.2 mmol/g on day 15 of incubation). Using denatured gradient gel electrophoresis (DGGE) it was observed that the microbial population dynamics of the microcosm depended on the stimulant. A decrease of bands indicated that the addition of Na-acetate and methanol had caused a decrease of bacterial diversity during the stimulation process compared to the control treatment (without stimulant).

Composition of Anopheles coluzzii and Anopheles gambiae microbiota from larval to adult stages

During their immature life stages, malaria mosquitoes are exposed to a wide array of microbes and contaminants from the aquatic habitats. Although prior studies have suggested that environmental exposure shapes the microbial community structure in the adult mosquito, most reports have focused on laboratory-based experiments and on a single mosquito epithelium, the gut. In this study, we investigated the influence of the breeding site on the development of the Anopheles coluzzii and Anopheles gambiae microbiota in natural conditions. We characterized bacterial communities from aquatic habitats, at surface microlayer and subsurface water levels, to freshly emerge adult mosquitoes using multiplexed 16S rRNA gene pyrosequencing and we separately analyzed the microbiota associated with the different epithelia of adult individual, midguts, ovaries and salivary glands. We found that the distribution of bacterial communities in the aquatic habitats differed according to the depth of water collections. Inter-individual variation of bacterial composition was large in larvae guts but adult mosquitoes from a same breeding site shared quite similar microbiota. Although some differences in bacterial abundances were highlighted between the different epithelia of freshly emerged An. coluzzii and An. gambiae, an intriguing feature from our study is the particular similarity of the overall bacterial communities. Our results call for further investigations on the bacterial population dynamics in the different tissues to determine the distinctive characteristics of each microbiota during the mosquito lifespan and to identify specific interactions between certain key phyla or species and the insect life history traits.

P-Cresol mineralization and bacterial population dynamics in a nitrifying sequential batch reactor

The ability of a nitrifying sludge to oxidize p-cresol was evaluated in a sequential batch reactor (SBR). p-Cresol was first transformed to p-hydroxybenzaldehyde and p-hydroxybenzoate, which were later mineralized. The specific rates of p-cresol consumption increased throughout the cycles. The bacterial population dynamics were monitored by using denaturing gradient gel electrophoresis (DGGE) and sequencing of DGGE fragments. The ability of the sludge to consume p-cresol and intermediates might be related to the presence of species such as Variovorax paradoxus and Thauera mechernichensis. p-Cresol (25 to 200mgC/L) did not affect the nitrifying SBR performance (ammonium consumption efficiency and nitrate production yield were close to 100% and 1, respectively). This may be related to the high stability observed in the nitrifying communities. It was shown that a nitrifying SBR may be a good alternative to eliminate simultaneously ammonium and p-cresol, maintaining stable the respiratory process as the bacterial community.

Effect of autochthonous bacteriocin-producing Lactococcus lactis on bacterial population dynamics and growth of halotolerant bacteria in Brazilian charqui

Charqui is a fermented, salted and sun-dried meat product, widely consumed in Brazil and exported to several countries. Growth of microorganisms in this product is unlikely due to reduced Aw, but halophilic and halotolerant bacteria may grow and cause spoilage. Charqui is a good source of lactic acid bacteria able to produce antimicrobial bacteriocins. In this study, an autochthonous bacteriocinogenic strain (Lactococcus lactis subsp. lactis 69), isolated from charqui, was added to the meat used for charqui manufacture and evaluated for its capability to prevent the growth of spoilage bacteria during storage up to 45 days. The influence of L. lactis 69 on the bacterial diversity during the manufacturing of the product was also studied, using denaturing gradient gel electrophoresis (DGGE). L. lactis 69 did not affect the counts and diversity of lactic acid bacteria during manufacturing and storage, but influenced negatively the populations of halotolerant microorganisms, reducing the spoilage potential. The majority of tested virulence genes was absent, evidencing the safety and potential technological application of this strain as an additional hurdle to inhibit undesirable microbial growth in this and similar fermented meat products.