Changes In Microbial Populations Research Articles

Effect of sulfate and lactate loading rates on the respiration process and microbial population changes measured by ecological indices.

In a sulfate reducing process, increasing loading rates and sulfide accumulation may induce population changes resulting in decreasing effectiveness of the process. Thus, the relationship between microbial metabolism changes and population dynamics was studied. An upflow anaerobic sludge blanket reactor was operated at different sulfate loading rates (SLR), from 290 to 981 mg SO4-S/L d at a constant carbon/sulfur ratio of 0.75. When the SLR was increased, the total organic carbon and sulfate consumption efficiencies decreased to nearly 30% and 25%, respectively. The acetate and propionate yields increased with increasing SLR and 385±7 mg sulfide-S/L d was reached. The ecological indices, determined by random amplified polymorphic DNA and denaturing gradient gel electrophoresis techniques, diversity and evenness were found to be constant, and similarity coefficient values remained higher than 76%. The results suggest that the microbial population changes were negligible compared with metabolic changes when SLR was increased. The sulfide accumulation did not modify the microbial diversity. The sequencing of 16S rRNA genes showed strains related to sulfate reducing, fermentation, and methanogenesis processes. The results indicated that the decreasing of effectiveness, under the experimental conditions tested, was dependent more on operational parameters than microbial changes.

Short-term differential adaptation to anaerobic stress via genomic mutations by Escherichia coli strains K-12 and B lacking alcohol dehydrogenase.

Microbial adaptations often occur via genomic mutations under adverse environmental conditions. This study used Escherichia coli ΔadhE cells as a model system to investigate adaptation to anaerobic conditions, which we then compared with the adaptive mechanisms of two closely related E. coli strains, K-12 and B. In contrast to K-12 ΔadhE cells, the E. coli B ΔadhE cells exhibited significantly delayed adaptive growth under anaerobic conditions. Adaptation by the K-12 and B strains mainly employed anaerobic lactate fermentation to restore cellular growth. Several mutations were identified in the pta or pflB genes of adapted K-12 cells, but mostly in the pta gene of the B strains. However, the types of mutation in the adapted K-12 and B strains were similar. Cellular viability was affected directly by severe redox imbalance in B ΔadhE cells, which also impaired their ability to adapt to anaerobic conditions. This study demonstrates that closely related microorganisms may undergo different adaptations under the same set of adverse conditions, which might be associated with the specific metabolic characteristics of each strain. This study provides new insights into short-term microbial adaptation to stressful conditions, which may reflect dynamic microbial population changes in nature.

Impact of Saline Water Treatments on Vegetative Propagation of Bambusa Vulgaris Var. Vulgaris

A nursery experiment was conducted to investigate the effect of saline water irrigation on the cuttings of Bambusa vulgaris var. vulgaris Schrad. and the changes in soil properties and soil microbial population was studied during the year 2009-10. The experiment was laid out in CRD. Ten treatments of saline water were prepared with EC of 0.20 dSm-1 to 4.0 dSm-1 by adding salts viz. CaCl2, MgSO4, NaHCO3 and NaCl in the ratio of 4:2:1:1 respectively. The highest sprouting percentage was found in irrigation water with the least EC (0.20 dSm-1) which was on par with treatments up to EC of 1.0 dSm-1. A decrease in sprouting percentage was found with the increase in EC. No sprouting under 3.0 dSm-1 and 4.0 dSm-1 was observed. In soil properties, an increase in soil EC and a non significant change in soil pH were found. The soil organic carbon and available nitrogen content decreased in treatments with the lower EC up to 1.0 dSm-1 while it increased in treatments with EC above 1.25 dSm-1. Available phosphorus recorded a non significant difference. Available potassium was found to increase with increasing saline treatments. A general decline in the population of fungi, actinomycetes and bacteria with the increase in EC levels was observed. Thus, for the successful vegetative propagation of Bambusa vulgaris the irrigation water should have an EC level up to 1.0 dSm-1.

The colonization dynamics of the gut microbiota in tilapia larvae.

The gut microbiota of fish larvae evolves fast towards a complex community. Both host and environment affect the development of the gut microbiota; however, the relative importance of both is poorly understood. Determining specific changes in gut microbial populations in response to a change in an environmental factor is very complicated. Interactions between factors are difficult to separate and any response could be masked due to high inter-individual variation even for individuals that share a common environment. In this study we characterized and quantified the spatio-temporal variation in the gut microbiota of tilapia larvae, reared in recirculating aquaculture systems (RAS) or active suspension tanks (AS). Our results showed that variation in gut microbiota between replicate tanks was not significantly higher than within tank variation, suggesting that there is no tank effect on water and gut microbiota. However, when individuals were reared in replicate RAS, gut microbiota differed significantly. The highest variation was observed between individuals reared in different types of system (RAS vs. AS). Our data suggest that under experimental conditions in which the roles of deterministic and stochastic factors have not been precisely determined, compositional replication of the microbial communities of an ecosystem is not predictable.

The effect of diet and environmental temperature on the faecal microbiota of farmed Tasmanian Atlantic Salmon (Salmo salarL.)

We investigated the changes in the faecal microbial population of the hindgut of farmed Atlantic salmon fed two commercial diets (A and B) over a 10-month period. At each sampling round, hindgut contents of 40 fish (20 per diet) were pooled according to diet and cultivated on selective agar. The functional status of all microbiota was assessed against 48 substrates using the PhPlate generalized microplate, which also yielded a metabolic capacity (MC) value for each microbiota. Virulence gene profiles of each microbiota were also investigated. The number of different bacterial groups between two diets varied slightly and increased as water temperature peaked at 18.5°C during summer. This however, was associated with an increase in Vibrio numbers and a decrease in lactic acid bacterial numbers. A shift in the functional status of gut microbiota was observed as temperature increased, which was coupled with a decrease in the MC-value of the microbiota in both diets. Of the 35 virulence genes tested from total DNA extract of the microbiota, only cdt and east1 were detected. Results indicate that temperature is the main driver of changes to the gut microbiota in farmed Tasmanian Atlantic salmon receiving these two diets.

An in vitro culture model to study the dynamics of colonic microbiota in Syrian golden hamsters and their susceptibility to infection with Clostridium difficile.

Clostridium difficile infections (CDI) are caused by colonization and growth of toxigenic strains of C. difficile in individuals whose intestinal microbiota has been perturbed, in most cases following antimicrobial therapy. Determination of the protective commensal gut community members could inform the development of treatments for CDI. Here, we utilized the lethal enterocolitis model in Syrian golden hamsters to analyze the microbiota disruption and recovery along a 20-day period following a single dose of clindamycin on day 0, inducing in vivo susceptibility to C. difficile infection. To determine susceptibility in vitro, spores of strain VPI 10463 were cultured with and without soluble hamster fecal filtrates and growth was quantified by quantitative PCR and toxin immunoassay. Fecal microbial population changes over time were tracked by 16S ribosomal RNA gene analysis via V4 sequencing and the PhyloChip assay. C. difficile culture growth and toxin production were inhibited by the presence of fecal extracts from untreated hamsters but not extracts collected 5 days post-administration of clindamycin. In vitro inhibition was re-established by day 15, which correlated with resistance of animals to lethal challenge. A substantial fecal microbiota shift in hamsters treated with antibiotics was observed, marked by significant changes across multiple phyla including Bacteroidetes and Proteobacteria. An incomplete return towards the baseline microbiome occurred by day 15 correlating with the inhibition of C. difficile growth in vitro and in vivo. These data suggest that soluble factors produced by the gut microbiota may be responsible for the suppression of C. difficile growth and toxin production.

Comparison of microbial communities and histological changes in Phase I rice straw-based Agaricus bisporus compost prepared using two composting methods

Rice straw is an important raw material for preparing Agaricus bisporus compost in China, and the size mushroom yield is largely determined by the quality of compost, which in turn is dependent on the microbial processes occurring during composting and the microbial populations inhabiting the mature compost. In this study, we compared the traditional composting method used in China with an aerated tunnel-based composting system through Phase I of the process. Phospholipid fatty acid (PLFA) analysis, used to monitor changes in the respective microbial populations, demonstrated a significant difference in the structure of the microbial communities and bacterial biomass associated with the two compost types. Chemical analysis of the degraded rice straw (RS) revealed that hemicellulose and silicate levels decreased more strongly in the aerated compared than in traditional non-aerated compost. Transmission electron microscopy (TEM), used to assess histological changes occurring in the stem tissue and cell walls of RS subjected to the two composting methods, showed that the aeration treatment resulted in more pronounced effects on stem structure. Composting using the aerated method also facilitated faster mycelial growth rates and higher yields of mushroom fruit bodies. Our data indicated that aeration-assisted composting of RS leads to improved degradation and assimilation of breakdown products by A. bisporus, and suggest that introduction of the process on a commercial scale in China has huge potential.

Application of Ozone in Full-Scale to Reduce Filamentous Bulking Sludge at Öresundsverket WWTP

The return sludge of one of the four treatment lines at Öresundsverket WWTP in Sweden was subjected to ozonation in full-scale to reduce filamentous bulking sludge. The biological nitrogen and phosphorus removal capacity along with effluent parameters were studied throughout the trial. Samples were also taken to track possible changes in microbial population due to ozone. 2.8–5.0 g O3 kg−1 treated SS−1 reduced the DSVI of the ozone-treated line from 170 to 100 mL g−1 and the reference line remained at 150 mL g−1. No adverse effect on the biological nitrification- or the phosphorus removal rates could be detected. The microbial population of the two lines did not exhibit any substantial changes which can be correlated to ozone addition.

Biodegradation of emulsified Mc252 oil in coastal salt marshes

On 05/22/10, emulsified form of MC 252oil was collected from Belle Pass near Port Fourchon in Lafourche Parish, LA and used for biodegradation studies. The objectives of this study were to determine the hydrocarbon composition of the emulsified oil, extent of biodegradation of emulsified oil and the change in microbial population. Soil cores were obtained from the salt marshes in Lafourche Parish, LA using aluminum core device and transferred to glass cores (15 cm dia × 100 cm long) and incubated inside a greenhouse. Approximately, 100 g of the emulsified oil was added to cores consistent with oil loadings observed in the field. Replicate cores were used to evaluate three treatment conditions; (i) natural attenuation with existing nutrient concentrations, (ii) nitrogen amendment and (iii) nitrogen + sulfate amendment. The cores were maintained with approximately 1” layer of synthetic seawater above sediment. For each treatment, cores were sacrificed for oil analysis every 30 days for the first three months (short-term fate) and after approximately a year (long-term fate). The cores were cut from the top and polycyclic aromatic hydrocarbons were analyzed from the soil sections 0–2 cm, 2–4 cm and 8–10 cm. Composition of the emulsified oil was characterized as the ratio of the compound analyzed to hopanes. Short-term incubations demonstrated limited biodegradation of key PAHs. Only phenanthrene biodegraded to any statistically significant extent in treatments over the first 3 months. Over the long-term (~1 year), biodegradation of phenanthrenes and dibenzothiophenes was observed and biodegradation extent was greater in fertilized treatments. Spontaneous breaking of emulsions was observed in several cores and this may precede biodegradation. Microbial community structure indicated diverse but different microbial populations in the three treatments.

Bioremediation of chlorimuron-ethyl-contaminated soil by Hansschlegelia sp. strain CHL1 and the changes of indigenous microbial population and N-cycling function genes during the bioremediation process

Long-term and excessive application of the herbicide chlorimuron-ethyl has led to soil degradation and crop rotation barriers. In the current study, we isolated bacterial strain Hansschlegelia sp. CHL1, which can utilize chlorimuron-ethyl as its sole carbon and energy source, and investigated its application in soil bioremediation. Indigenous microbial populations and N-cycling function in the soil were also investigated during the bioremediation process by monitoring the copy numbers of bacterial and fungal marker genes, as well as N-cycling functional genes (nifH, amoA, nirS, and nirK). Results showed that >95% of chlorimuron-ethyl could be degraded within 45 days in soils inoculated with CHL1. Inoculation at two time points resulted in a higher remediation efficiency and longer survival time than a single inoculation. At the end of the 60-day incubation, the copy numbers of most indicator genes were recovered to the level of the control, even in the single-inoculation soils. A double inoculation was necessary for recovery of nifH. However, the abundance of nirK and ammonia-oxidizing bacterial genes were significantly inhibited regardless of inoculum. The results suggested that CHL1 is effective for the remediation of chlorimuron-ethyl-contaminated soil, and could partially reduce the toxic effects of chlorimuron-ethyl on soil microorganisms.

Assessing non-digestible compounds in apple cultivars and their potential as modulators of obese faecal microbiota in vitro

The health benefits of apple bioactive compounds have been extensively reported. However, only few studies have focused on bioactive compounds that are not absorbed and metabolised during gastrointestinal digestion and can induce changes in microbial populations of faeces. We have characterised Braeburn, Fuji, Gala, Golden Delicious, Granny Smith, McIntosh and Red Delicious cultivars and found significant differences for extractable phenolics (1.08–9.2mg/g) non-extractable proanthocyanidins (3.28–5.7mg/g), and dietary fibre (20.6–32.2%) among cultivars with Granny Smith having the highest contents. Granny Smith was used after in vitro digestion for fermentation of faeces from diet-induced obese mice. Results showed that relative abundances of Firmicutes, Bacteroidetes, Enterococcus, Enterobacteriaceae, Escherichia coli, and Bifidobacterium in apple cultured faeces tended to resemble the abundance in faeces from lean mice with increased trend in the production of butyric acid. These results suggest that apple non-digestible compounds might help to re-establish a disturbed microbiota balance in obesity.

Metatranscriptomics of the Human Oral Microbiome during Health and Disease

ABSTRACTThe human microbiome plays important roles in health, but when disrupted, these same indigenous microbes can cause disease. The composition of the microbiome changes during the transition from health to disease; however, these changes are often not conserved among patients. Since microbiome-associated diseases like periodontitis cause similar patient symptoms despite interpatient variability in microbial community composition, we hypothesized that human-associated microbial communities undergo conserved changes in metabolism during disease. Here, we used patient-matched healthy and diseased samples to compare gene expression of 160,000 genes in healthy and diseased periodontal communities. We show that health- and disease-associated communities exhibit defined differences in metabolism that are conserved between patients. In contrast, the metabolic gene expression of individual species was highly variable between patients. These results demonstrate that despite high interpatient variability in microbial composition, disease-associated communities display conserved metabolic profiles that are generally accomplished by a patient-specific cohort of microbes.

Metagenomic analysis for identifying Kimchi sp. during the industrial-scale batch fermentation

Metagenome analysis was used to monitor changes in microbial population during the industrial-scale batch fermentation period (0, 15 days and 2 years). Genomic DNA was extracted from Bachu-Kimchi samples and was sequenced using GS Junior Titanium system, which yielded a total 6886, 6271, and 6621 reads from 0, 15 days and 2 years samples, respectively. Phylogenetic analysis based on 16S rRNA sequences showed clearly that microbial population was changed depending on the fermentation process (initial, rancid, and over-ripening stage). Wessella sp. and Leuconostoc sp. became the predominant group in microbial community at the optimum-rancid stage (15 days), but as the fermentation progressed more, the abundance of Lactobacillus sp. and Bacillus sp. increased (2 years). Moreover, the specific kimchi microbes in the industrial-scale fermentation process were isolated: Leuconostoc mesenteroides, Lactobacillus sakei, Lactobacillus plantarum, and Weissella koreensis.

Effects of long-term diazinon exposure on some immunological and haematological parameters in rainbow trout Oncorhynchus mykiss (Walbaum, 1792)

Metagenome analysis was used to monitor changes in microbial population during the industrial-scale batch fermentation period (0, 15 days and 2 years). Genomic DNA was extracted from Bachu-Kimchi samples and was sequenced using GS Junior Titanium system, which yielded a total 6886, 6271, and 6621 reads from 0, 15 days and 2 years samples, respectively. Phylogenetic analysis based on 16S rRNA sequences showed clearly that microbial population was changed depending on the fermentation process (initial, rancid, and over-ripening stage). Wessella sp. and Leuconostoc sp. became the predominant group in microbial community at the optimumrancid stage (15 days), but as the fermentation progressed more, the abundance of Lactobacillus sp. and Bacillus sp. increased (2 years). Moreover, the specific kimchi microbes in the industrial-scale fermentation process were isolated: Leuconostoc mesenteroides, Lactobacillus sakei, Lactobacillus plantarum, and Weissella koreensis.

Investigation of Colony Forming Unit (CFU) of Microorganisms in the Paprika-grown Greenhouses Using Open and Closed Soilless Culture Systems

본 연구는 순환식과 비순환식 수경재배 온실 내 특정 구역에서 잠재적인 병발생 가능성을 추정하기 위하여 미생물 시료의 채취 및 배양을 통하여 집락형성단위수(CFU)를 분석하였다. 시료의 채취는 배지를 기준으로 각 구역별 3cm 간격으로 <TEX>$25cm^2$</TEX>의 면적에 대해 4개의 구역을 각 온실별로 3회 반복하여 이루어졌다. 비순환식과 순환식 수경재배 온실에서 암면과 코이어를 배지로 사용하는 각 2개 농가를 조사대상으로 하였다. 진균류의 경우 비순환식 수경재배 온실에서 유의적으로 높은 수준의 집락형성단위수(CFU)가 관찰되었다. 세균류의 경우는 유의적인 차이는 관찰되지 않았지만, 순환식 수경재배 온실이 비교적 낮은 경향을 나타냈다. 위치 별 CFU의 비교에서는 순환식과 비순환식 모두 배액의 발생에 따른 환경조건의 변화가 적은 배지 부분에서 가장 낮은 수준의 CFU가 관찰되었다. 주성분 분석결과 온실 내 배액의 이동 경로 상에서 수집된 시료가 미생물의 개체수 변화에 많이 기여하고 있는 것으로 판단되었다. 순환식 수경재배 온실은 비순환식 수경재배 온실에 비해 미생물 증식억제에 유리한 조건에 있으며, 이는 외부 환경에 비해 비교적 단순한 생태계로 구성된 온실의 조건을 고려해 보았을 때 잠재적인 병 발생 가능성이 상대적으로 낮음을 의미한다. This study was conducted to compare colony forming unit (CFU) of microorganisms in closed and open soilless culture systems for estimating the possibility for potential disease occurrence. Samples were collected at four different positions in four commercial greenhouses with closed or open soilless culture system using rock wool or coir as substrate, respectively. The distance between sampling positions was 3 cm starting from the substrate and the surface area of each position was <TEX>$25cm^2$</TEX>. The CFU of fungi was significantly higher in the open system, while that of bacteria was not significantly different but showed relatively lower in the closed system. Samples collected at the plastic surface of the substrates where little environmental effects occurred from drainage showed lower CFU than any other positions. The principal component analysis showed that samples collected on the drainage pathway highly affected the changes in microbial population in the greenhouse. These results indicated that greenhouses with closed soilless culture are expected to have more advantageous conditions for restraining the microbial growth, resulting in the lower potential of disease occurence in greenhouse ecosystem.

염소 소독에 의한 저장빗물수질 유지효과 연구

The purpose of this study is to monitor the rainwater flowing from the roof of buildings and to maximize the effectiveness of the rainwater storage. This study also analyses the changes in rainwater characteristics before and after subsequent chlorination disinfection. The stored rainwater was disinfected by chlorine and then analyzed for COD, TN, TP, enteric bacteria, and general microbial population changes over time. There was an observed 99% reduction of enteric bacteria and common microbes within two weeks after chlorine injection. Thus, chlorine disinfection of rainwater improves water quality for long-term storage and future use.

Biochar application to hardrock mine tailings: Soil quality, microbial activity, and toxic element sorption

Waste rock piles from historic mining activities remain unvegetated as a result of metal toxicity and high acidity. Biochar has been proposed as a low-cost remediation strategy to increase soil pH and reduce leaching of toxic elements, and improve plant establishment. In this laboratory column study, biochar made from beetle-killed pine wood was assessed for utility as a soil amendment by mixing soil material from two mine sites collected near Silverton, Colorado, USA with four application rates of biochar (0%, 10%, 20%, 30% vol:vol). Columns were leached seven times over 65days and leachate pH and concentration of toxic elements and base cations were measured at each leaching. Nutrient availability and soil physical and biological parameters were determined following the incubation period. We investigated the hypotheses that biochar incorporation into acidic mine materials will (1) reduce toxic element concentrations in leaching solution, (2) improve soil parameters (i.e. increase nutrient and water holding capacity and pH, and decrease compaction), and (3) increase microbial populations and activity. Biochar directly increased soil pH (from 3.33 to 3.63 and from 4.07 to 4.77 in the two materials) and organic matter content, and decreased bulk density and extractable salt content in both mine materials, and increased nitrate availability in one material. No changes in microbial population or activity were detected in either mine material upon biochar application. In leachate solution, biochar increased base cations from both materials and reduced the concentrations of Al, Cd, Cu, Pb, and Zn in leachate solution from one material. However, in the material with greater toxic element content, biochar did not reduce concentrations of any measured dissolved toxic elements in leachate and resulted in a potentially detrimental release of Cd and Zn into solution at concentrations above that of the pure mine material. The length of time of effectiveness and specific sorption by biochar is variable by element and the toxic element concentration and acidity of the initial mine material.

Changes in Microbial Population of Palm Oil Mill Effluent Polluted Soil Amended with Chicken Droppings and Cow Dung

Aim of Study : To assess changes in microbial population in palm oil mill effluent (POME) polluted soil amended with chicken droppings and cow dung. Study Design : 32 plots measuring 4 m

Microbial existence in controlled habitats and their resistance to space conditions.

The National Research Council (NRC) has recently recognized the International Space Station (ISS) as uniquely suitable for furthering the study of microbial species in closed habitats. Answering the NRC’s call for the study, in particular, of uncommon microbial species in the ISS, and/or of those that have significantly increased or decreased in number, space microbiologists have begun capitalizing on the maturity, speed, and cost-effectiveness of molecular/genomic microbiological technologies to elucidate changes in microbial populations in the ISS and other closed habitats. Since investigators can only collect samples infrequently from the ISS itself due to logistical reasons, Earth analogs, such as spacecraft-assembly clean rooms, are used and extensively characterized for the presence of microbes. Microbiologists identify the predominant, problematic, and extremophilic microbial species in these closed habitats and use the ISS as a testbed to study their resistance to extreme extraterrestrial environmental conditions. Investigators monitor the microbes exposed to the real space conditions in order to track their genomic changes in response to the selective pressures present in outer space (external to the ISS) and the spaceflight (in the interior of the ISS). In this review, we discussed the presence of microbes in space research-related closed habitats and the resistance of some microbial species to the extreme environmental conditions of space.

Injury and Viability Loss of Escherichia coli O157:H7, Salmonella, Listeria Monocytogenes and Aerobic Mesophilic Bacteria in Apple Juice and Cider Amended with Nisin-Edta

For health reasons, people are consuming fresh juices or minimally processed fruit and vegetable juices, thereby, exposing themselves to the risk of foodborne illness if such juices are contaminated with bacteria pathogens. Behavior of aerobic mesophilic bacteria, Escherichia coli O157:H7, L. monocytogenes and Salmonella cells at 104 CFU/ml in apple cider (pH 3.9) and apple juice (pH 3.6), amended with nisin (500 IU/ml)+ethylene diaminetetraacetic acid (EDTA, 0.02 M) combination treatment and storage at 5°C and 10°C for 10 days as well as 22oC for 16 h was investigated. Populations of aerobic mesophilic bacteria increased in untreated apple cider stored at 5°C and 10°C for 10 days while E. coli O157:H7, L. monocytogenes and Salmonella slightly declined. A slight increase for E. coli O157:H7, L. monocytogenes and Salmonella in juices stored at room temperature (22°C) was observed. Treatment of juices with nisin+EDTA led to higher inactivation of bacterial populations including inoculated populations of E. coli O157:H7, L. monocytogenes and Salmonella. The surviving populations determined within 10 to 30 min of treatment include 18% of injured cells. And leakage of UV- absorbing materials were higher in samples containing the injured bacteria. The injured populations did not recover during storage at 5 or 22°C. Waiting up to 4 h before refrigeration of treated samples and leaving treated refrigerated samples at room temperature for up to 4 h did not cause significant changes in microbial populations. Addition of nisin+EDTA combination in unpasteurized apple cider or apple juice as a natural antimicrobial will improve the microbial safety of the juices. However, treatment of juices with nisin+EDTA combination is still subject to regulatory approval by the FDA.