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PubMed2001

Structure of microbial communities in activated sludge: potential implications for assessing the biodegradability of chemicals.

Various methods used to assess the biodegradability of chemicals often employ activated sludge as an inoculum since chemicals that ultimately enter the environment are often discharged through wastewater. Differences in the structure and function of activated sludge microbial communities that may complicate interpretation of biodegradation tests could arise from differences in wastewater composition, wastewater treatment plant (WWTP) operation, or manipulations done after collection of the activated sludge. In this study, various methods were used to characterize the structure of microbial communities found in freshly collected activated sludge from WWTPs in Japan, Europe, and the United States, as well as sludge that had been continuously fed either sewage or a glucose-peptone mixture for several weeks after collection. Comparisons of biomass levels, whole-community substrate utilization (determined using Biolog GN and GP plates), and phospholipid fatty acid (PLFA) profiles indicated there were both geographical and temporal differences among freshly collected activated sludge samples. Moreover, marked shifts in the structure of activated sludge microbial communities occurred upon continuous cultivation in the laboratory for 5 weeks using a glucose-peptone feed. These shifts were evident from whole-community substrate utilization and PLFA profiles as well as differences in the profiles of 16S rDNA genes from numerically dominant populations obtained by denaturing gradient gel electrophoresis and terminal restriction fragment analyses. Further studies are needed to better define the variability within and between activated sludge from wastewater treatment plants and laboratory reactors and to assess the impact of such differences on the outcome of biodegradability tests.

Bacteria↗
PubMed2000

Seasonal microbial community dynamics in a flowerpot-using personal composting system for disposal of household biowaste.

Microbial community dynamics in a flowerpot-using solid biowaste composting (FUSBIC) process were monitored seasonally by quinone profiling and conventional microbiological methods. The FUSBIC system, which consisted of three flowerpots (14 L or 20 L capacity) with 5-6 kg each of a soil-compost mixture (SCM) as the primary reactors, was loaded daily with household biowaste from November 1998 to October 1999. The monthly average waste reduction rate was 88.2% for the 14-L system and 92.5% for the 20-L system on a wet weight basis. The direct total microbial count detected in the 14-L primary reactors ranged from 4.5 to 9.6x10(11) cells.g(-1) of dry wt of SCM, and the viable count of aerobic heterotrophic bacteria recovered on agar plates at 28 degrees C varied from 1.9 to 5.7x10(11) CFU.g(-1) of dry wt. The quinone content of SCM samples from the 14-L and 20-L systems ranged from 160 to 353 nmol.g(-1) of dry SCM. Ubiquinones, unsaturated menaquinones, and partially saturated menaquinones constituted 15.0-36.4, 14.8-22.0, and 41.8-61.6 mol% of the total content, respectively. The major quinone types detected were usually MK-8(H(2)), MK-9(H(2)), and Q-10. Variations in quinone profiles were evaluated numerically by using two parameters, the dissimilarity index (D) and microbial divergence index (MD(q)). The upper limit of seasonal changes in the microbial community structure was about 30% as expressed by D values. The MD(q) values calculated ranged from 18 to 22. A significant positive correlation was found between seasonal temperature and bacterial populations containing partially saturated menaquinones. These results indicated that the FUSBIC system contained highly diverse microbial populations that fluctuated to some extent depending on seasonal temperature. Members of the Actinobacteria were suggested to be the major constituents of the total population present.

Journal Article↗
PubMed2006

Effects of the phenylurea herbicide diuron on natural riverine microbial communities in an experimental study.

The effects of the phenylurea herbicide diuron (10 microgl(-1)) on natural riverine microbial communities were investigated using a three-week laboratory microcosm study. During the first six days, a latency period was observed both in the algal and the bacterial communities despite favorable abiotic conditions and independently of diuron exposure. From the second week, an intense algal bloom (chlorophyll a concentrations and cell abundances) was observed in the uncontaminated microcosms but not in the treated microcosms. The bloom stimulated the bacterial community and led to an increase in heterotrophic bacterial production ([3H]thymidine incorporation), activity (CTC reduction) and cell abundance. In parallel, shifts in bacterial community composition were recorded by polymerase chain reaction (PCR)-temporal temperature gradient gel electrophoresis (TTGE) analysis, whereas no major variation was detected using the fluorescent in situ hybridization (FISH) method. In the treated microcosms, the diuron acted not by damaging the initial communities but by inhibiting the algal bloom and indirectly maintaining constant bacterial conditions throughout the experiment. These inhibitory effects, which were recorded in terms of abundance, activity and diversity, suggest that exposure to diuron can decrease the recovery capacities of microbial communities and delay the resumption of an efficient microbial food web despite favorable environmental conditions.

Chlorophyll↗
PubMed2005

Changes in soil microbial community composition induced by cometabolism of toluene and trichloroethylene.

The effects of trichloroethylene (TCE) on microbial community composition were analyzed by reverse sample genome probing. Soil enrichments were incubated in dessicators containing an organic phase of either 1 or 10% (w/w) toluene in vacuum pump oil, delivering constant equilibrium aqueous concentrations of 16 and 143 mg/l, respectively. Increasing the equilibrium aqueous concentration of TCE from 0 to 10 mg/l led to shifts in community composition at 16, but not at 143 mg/l of toluene. In closed system co-degradation studies, TCE at an aqueous concentration of 1 mg/l was effectively degraded by toluene-degrading soil enrichments once the aqueous toluene concentration dropped below 25 mg/l. Little TCE degradation was observed at higher toluene concentrations (50-250 mg/l). The results indicate that TCE changes microbial community composition under conditions where it is being actively metabolized.

Biodegradation, Environmental↗
PubMed2006

Microbial colonization of beech and spruce litter--influence of decomposition site and plant litter species on the diversity of microbial community.

The present study was conducted to investigate the effect of decomposition site and plant litter species on the colonizing microbial communities. For this, litter bag technique using beech and spruce litter was combined with RNA-based fingerprinting and cloning. Litter bags were incubated for 2 and 8 weeks in the Ah horizon of beech and beech-spruce mixed forest sites. Although sugars and starch were rapidly lost, lignin content increased by more than 40% for beech and more than doubled for spruce litter at both soil sites at the end of the experiment. Denaturing gradient gel electrophoresis analysis of 16S and 18S rRNA RT-PCR products was used for screening of differences between bacterial and fungal communities colonizing the two litter types. Development of the microbial community over time was observed to be specific for each litter type and decomposition site. RT-PCR products from both litter types incubated in beech-spruce mixed forest site were also cloned to identify the bacterial and fungal colonizers. The 16S rRNA clone libraries of beech litter were dominated by gamma-proteobacterial members, whereas spruce libraries were mainly composed of alpha-, beta-, and gamma-proteobacterial members. Ascomycota members dominated the 18S rRNA clone libraries. Clones similar to Zygomycota were absent from spruce, whereas those similar to Basidiomycota and Glomeromycota were absent from beech libraries. Selective effects of litter quality were observed after 8 weeks. The study provides an insight into the bacterial and fungal communities colonizing beech and spruce litter, and the importance of litter quality and decomposition site as key factors in their development and succession.

Bacteria↗
PubMed2002

Microbial community dynamics during start-up of acidogenic anaerobic reactors.

Start-up of two acidogenic reactors under mesophilic (37 degrees C) and thermophilic (55 degrees C) conditions was carried out with methanogenic granular sludge as an inoculum and dairy wastewater as feed. During these 71 days of the start-up period, microbial community dynamics in these two acidogenic reactors, as monitored by denaturing gradient gel electrophoresis (DGGE) and dot-blot hybridization with group-specific oligonucleotide probes, was correlated to reactor performance. Due to pH drop to 5.5, DGGE community fingerprints for domains Bacteria and Archaea populations showed significant shifts after 13 days of operation, and this change was accompanied with an increase in volatile fatty acid production, a decrease in methane formation, and rapid sludge disintegration. Dot-blot hybridization results further indicated that the decrease in methane production was related to the decrease in Archaea population in particular with methanogens from 34.1% of total 16S-rRNA in the seed sludge to 8% within the first 13 days, and to 2-5% at day 71. Among the methanogens monitored, the class Methanomicrobiales was the most abundant followed up by Methanobacteriales and Methanococcales. Due to an elevated temperature, the microbial community change was more significant and rapid in the thermophilic reactor than in the mesophilic reactor. Significant microbial population changes took place at the first 13 days for both reactors, but a longer period up to 71 days was required to establish a microbial community with a stable metabolic activity.

Animals↗
PubMed2005

Oral microbial communities in sickness and in health.

The relationship between humans and their oral microflora begins shortly after birth and lasts a lifetime. Up until fairly recently, the associations between the host and oral bacteria were considered in terms of a multiplicity of single species interactions. However, it is becoming more apparent that the oral microbes comprise a complex community, and that oral health or disease depends on the interface between the host and the microbial community as a whole. Although it is important to continue studies of the pathogenic properties of specific microbes, these are relevant only in the context of the properties of the community within which they reside. Understanding the microbial communities that drive sickness or health is a key to combating human oral diseases.

Bacteria↗
PubMed2004

Considering the complexity of microbial community dynamics in food safety risk assessment.

The potential for competitive inhibition to limit the growth of microbial pathogens in food raises questions about the external validity of typical predictive microbiology studies and suggests the need to consider microbial community dynamics in food safety risk assessment. Ecological theory indicates, however, that community dynamics are highly complex and may be very sensitive to initial conditions and random variation. Seemingly incongruous empirical results for Escherichia coli O157:H7 in ground beef are shown to be consistent with a simple theoretical model of interspecific competition. A potential means of incorporating community-level microbial dynamics into the food safety risk assessment process is explored.

Antibiosis↗
PubMed2002

Histopathological methods for the investigation of microbial communities associated with disease lesions in reef corals.

AIMS: To determine the spatial structure of microbial communities associated with disease lesions of reef corals (Scleractinia). METHODS AND RESULTS: Agarose pre-embedding preserved the structure of the disease lesion and surrounding tissues prior to demineralization of the carbonate exoskeleton and embedding in resin. Fluorescence in situ hybridization (FISH) was used to localize bacteria in the lesions of various diseases. CONCLUSIONS: The techniques successfully preserved the in situ spatial structure of degenerated coral tissues. In one case (white plague disease), significant bacterial populations were found only in fragmented remnants of degenerated coral tissues at the lesion boundary that would not have been detected using conventional histopathological techniques. SIGNIFICANCE AND IMPACT OF THE STUDY: Determining the composition, spatial structure and dynamics of microbial communities within the disease lesions is necessary to understand the process of disease progression. The methods described may be applicable to a wide range of diseases involving necrotic lesion formation and requiring extensive tissue processing, such as skeleton demineralization.

Adaptation, Physiological↗
PubMed2005

Potential application of ribosomal intergenic spacer analysis to the microbial community analysis of agronomic products.

Ribosomal intergenic spacer analysis (RISA) has been applied to the microbial community analysis of agronomic products in combination with a simple and rapid DNA extraction method, consisting of a one-step extraction and two-step purification, for a variety of agronomic products. RISA appears to be a useful tool for the study of the community structures of food-associated microbes and their use as a unique fingerprinting signature for each agronomic product. Sequencing analyses of amplicons generated from RISA suggest that this method can detect conventional microbes. In the case of RISA of wasabi paste DNA, the sequences of the amplicons showed high similarity to the plant pathogen Xanthomonas campestris and the soil bacterium Bacillus subtilis, whereas several food-associated bacteria (Lactococcus lactis, Lactococcus raffinolactis, and Lactococcus sakei) were detected using this technique in sausage DNA. Unexpectedly, the sequencing analyses also revealed the presence of several microbes that possessed high similarity to human bacterial pathogens such as Weissella confusa and Yersinia pestis. The results suggest that RISA will be a useful method for routine microbial community analysis in agronomic products.

Bacteria↗
PubMed2005

Soil microbial community response to land use change in an agricultural landscape of western Kenya.

Tropical agroecosystems are subject to degradation processes such as losses in soil carbon, nutrient depletion, and reduced water holding capacity that occur rapidly resulting in a reduction in soil fertility that can be difficult to reverse. In this research, a polyphasic methodology has been used to investigate changes in microbial community structure and function in a series of tropical soils in western Kenya. These soils have different land usage with both wooded and agricultural soils at Kakamega and Ochinga, whereas at Ochinga, Leuro, Teso, and Ugunja a replicated field experiment compared traditional continuous maize cropping against an improved N-fixing fallow system. For all sites, principal component analysis of 16S rRNA gene denaturing gradient gel electrophoresis (DGGE) profiles revealed that soil type was the key determinant of total bacterial community structure, with secondary variation found between wooded and agricultural soils. Similarly, phospholipid fatty acid (PLFA) analysis also separated wooded from agricultural soils, primarily on the basis of higher abundance of monounsaturated fatty acids, anteiso- and iso-branched fatty acids, and methyl-branched fatty acids in the wooded soils. At Kakamega and Ochinga wooded soils had between five 5 and 10-fold higher levels of soil carbon and microbial biomass carbon than agricultural soils from the same location, whereas total enzyme activities were also lower in the agricultural sites. Soils with woody vegetation had a lower percentage of phosphatase activity and higher cellulase and chitinase activities than the agricultural soils. BIOLOG analysis showed woodland soils to have the greatest substrate diversity. Throughout the study the two functional indicators (enzyme activity and BIOLOG), however, showed lower specificity with respect to soil type and land usage than did the compositional indicators (DGGE and PLFA). In the field experiment comparing two types of maize cropping, both the maize yields and total microbial biomass were found to increase with the fallow system. Moreover, 16S rRNA gene and PLFA analyses revealed shifts in the total microbial community in response to the different management regimes, indicating that deliberate management of soils can have considerable impact on microbial community structure and function in tropical soils.

Agriculture↗
PubMed2005

Start-up of bio-hydrogen production reactor seeded with sewage sludge and its microbial community analysis.

Start-up of a continuously stirred tank reactor for bio-hydrogen production under different initial organic loading rate (OLR) of 3, 7 and 10 kgCOD/m3 d, respectively, was carried out with sewage sludge as inoculum. Molasses wastewater was used as substrate and hydraulic retention time was kept at 6 h. This study aimed to assess OLR on the formation of fermentation types and the structure of microbial communities during the start-up period. It was found that at an initial OLR of 7 kgCOD/m3 d and an initial biomass of 6.24 gVSS/L, an equilibrial microbial community of ethanol-type fermentation could be established within 30 days. The observed average specific hydrogen production rate was 276 mLH2/gVSS d, which was 40% higher than that of the one acclimated with 3 kgCOD/m3 d. Based on denaturing gradient gel electrophoresis profiles, significant microbial population shifts took place at the first 15 days, but a longer period up to 30 days was required to establish a microbial community with stable metabolic activity.

Bacteria↗
PubMed2006

Long-term monitoring of the succession of a microbial community in activated sludge from a circulation flush toilet as a closed system.

The microbial diversity and community succession of a circulation flush toilet were investigated by terminal restriction fragment length polymorphism and cloning analyses. Clonal libraries of 16S rRNA gene on day 3 and day 127 were constructed. On day 3, 102 clones were sequenced; Proteobacteria and Bacteroidetes accounted for 27% and 45%, respectively. On day 127, Proteobacteria had increased to 43% and Bacteroidetes had decreased to 26% of a total of 100 clones. Terminal restriction fragment length polymorphism peaks were identified by in silico analysis of clone libraries. The relative abundances of Nitrosomonas increased from 1% to 6% with commencement of nitrification and denitrification. Similarly, the relative abundance of terminal restriction fragments generated from Xanthomonas increased from 3% to 10%. Therefore, these bacteria could play a prominent role in this process. To reveal the relationship between stability of the microbial community and performance of the system, microbial community succession was visualized by multidimensional scaling analysis. The microbial community structure changed markedly, particularly during the start-up period of the system. The plots then became stable after the start of nitrification and denitrification. This result suggests that the succession of microbial community structure had a correlation with the performance of the system.

Bacteroidetes↗
PubMed2005

Impacts on microbial communities and cultivable isolates from groundwater contaminated with high levels of nitric acid-uranium waste.

Microbial communities were characterized at contaminated sites that had elevated levels of nitrate, nickel, aluminum, and uranium (up to 690 mM, 310 microM, 42 mM, and 30 microM, respectively). The bacterial community structure based upon clonal libraries of the SSU rRNA genes (screened clones = 876) was diverse at the background site, but the three acidic samples had decreased diversity and the majority of clones were closely related to Azoarcus and Pseudomonas species. Arthrobacter and Novosphingobium sequences were recovered from the background samples but not the acidic sites, and similar pseudomonad populations were present at the background and acidic sites albeit at different relative abundances. Heterologous sequence coverage analyses indicated the microbial communities at the contaminated sites were very similar (p = 0.001) but different from the background site. Bacterial isolates (n = 67) classified as beta-or gamma-Proteobacteria, high G+C Gram-positive or low G+C Gram-positive were obtained from the background and one contaminated sample, and some of the isolates had less than 95% sequence identity with previously observed microorganisms. Despite variations in nitrate and heavy metal levels and different proximities to the source ponds, the three acidic samples had similar microbial populations. However, the least contaminated site (lowest nitrate and aluminum) had increased diversity compared to the other acidic samples. The results suggested that the combined contamination has decreased the microbial diversity, and Azoarcus populations were observed at a drastically increased frequency compared to the background site that had a more even distribution of multiple taxa.

Aluminum↗
PubMed2006

Dynamics of a pig slurry microbial community during anaerobic storage and management.

The microbial community of a pig slurry on a farm was monitored for 6 months using both molecular and cultural approaches. Sampling was carried out at all the different stages of effluent handling, from the rearing build-up to slurry spreading. Total DNA of each sample was extracted and analyzed by PCR-single-strand conformation polymorphism (SSCP) analysis using primers targeting the 16S rRNA genes from the archaeal and bacterial domains and also the Eubacterium-Clostridium, Bacillus-Streptococcus-Lactobacillus, and Bacteroides-Prevotella groups. A comparison of the SSCP profiles showed that there were rapid changes in the dominant bacterial community during the first 2 weeks of anaerobic storage and that the community was relatively stable thereafter. Several bacterial populations, identified as populations closely related to uncultured Clostridium and Porphyromonas and to Lactobacillus and Streptococcus cultured species commonly isolated from pig feces, remained present and dominant from the rearing build-up to the time of spreading. Enumeration of fecal indicators (enterococci and Escherichia coli) performed in parallel using cultural methods revealed the same trends. On the other hand, the archaeal community adapted slowly during pig slurry storage, and its diversity increased. A shift between two hydrogenotrophic methanogenic Methanobrevibacter populations from the storage pit to the pond was observed. Microorganisms present in pig slurry at the time of spreading could not be detected in soil after spreading by either molecular or cultural techniques, probably because of the detection limit inherent in the two techniques.

Anaerobiosis↗
PubMed2001

[Composting process of municipal solid waste with high effective complex microbial community].

The effects of high effective complex microbial community (MECMC) in a combination composting process of municipal solid waste (MSW) and sludge were examined through inspecting biomass, temperature, organic matter, the carbon, nitrogen ration (C/N). Composting was performed under such conditions: The ratio of MSW:sewage:sawdust:composting of 45:25:15:15 (W/W) and organic matter of 60%, total N of 1.4%, total P of 0.69%, total K of 1.25%, original moisture of 58.5%, original ratio of C/N of 30, aration flow of 0.8 L/min.kg(volatile organic matter). The rates of adding HECMC to treatment 1, treatment 2 and treatment 3 were 2%, 3%, 5% respectively. Control experiment added 3% inactive HECMC. The day of MSW and sludge mature in control experiment, treatment 1, treatment 2 and treatment 3 were 30, 24, 18 and 12, respectivly. This indicated HECMC were effective to compose organic matter and speedup composting change into humus. There are many active bacteria in composting which are favorable for soil.

Bacteria↗
PubMed1998

Interactions between metals and microbial communities in New Bedford Harbor, Massachusetts.

The fate of toxic metals in marine sediments depends on a combination of the physical, chemical, and biologic conditions encountered in any given environment. These conditions may vary dramatically, both spatially and temporally, in response to factors ranging from seasonal changes and storm events to human activities such as dredging or remediation efforts. This paper describes a program designed to evaluate the interrelationships between the microbial community and pollutants in the New Bedford Harbor, Massachusetts, area, a U.S. Environmental Protection Agency designated Superfund site. Research has focused on establishing distributional relationships between contaminant metals, fluxes of metals between sediments and the overlying water, changes in microbial diversity in response to metals, and potential use of the microbial community as a biomarker of contaminant availability. This research has shown that a significant flux of metals to the water column is mediated by benthic biologic activity, and that microbial communities may be a responsive marker of contaminant stress. A combination of biogeochemical studies and the use of molecular tools can be used to improve our understanding of the fate and effect of heavy metals released to aquatic systems.

Animals↗
PubMed2005

Reduction of perchlorate and nitrate by microbial communities in vadose soil.

Perchlorate contamination is a concern because of the increasing frequency of its detection in soils and groundwater and its presumed inhibitory effect on human thyroid hormone production. Although significant perchlorate contamination occurs in the vadose (unsaturated) zone, little is known about perchlorate biodegradation potential by indigenous microorganisms in these soils. We measured the effects of electron donor (acetate and hydrogen) and nitrate addition on perchlorate reduction rates and microbial community composition in microcosm incubations of vadose soil. Acetate and hydrogen addition enhanced perchlorate reduction, and a longer lag period was observed for hydrogen (41 days) than for acetate (14 days). Initially, nitrate suppressed perchlorate reduction, but once perchlorate started to be degraded, the process was stimulated by nitrate. Changes in the bacterial community composition were observed in microcosms enriched with perchlorate and either acetate or hydrogen. Denaturing gradient gel electrophoresis analysis and partial sequencing of 16S rRNA genes recovered from these microcosms indicated that formerly reported perchlorate-reducing bacteria were present in the soil and that microbial community compositions were different between acetate- and hydrogen-amended microcosms. These results indicate that there is potential for perchlorate bioremediation by native microbial communities in vadose soil.

Acetates↗