Sampling culturable heterotrophs from microcosms: a statistical analysis.

The contributions of different sources of error in sampling mixed and unmixed bacterial microcosms were evaluated by using analysis of variance. Culturable heterotrophic bacteria from a turbid freshwater impoundment were sampled from 9-liter tanks that were unagitated or mixed with magnetic stirrers or pumps and from dilution bottles that were unagitated or agitated with a mechanical shaker. Axenic cultures of Enterobacter aerogenes were also sampled from manually shaken test tubes. In both agitated and unagitated tanks and in unagitated dilution bottles, dilutions made from the same sampling pipette were significantly different, showing a clumping of bacteria on the scale of millimeters. Also, microcosms within a single experiment differed from one another by a large margin. Dilution mean squares and tank or bottle mean squares were homogeneous for all types of tanks and unagitated bottles, indicating that the gentle mixing provided by pumps and stir bars did not reduce either millimeter scale or intermicrocosm variability over what prevailed in unagitated microcosms. By contrast, the vigorously shaken bottles and test tubes showed no millimeter scale variability. Intermicrocosm variability was undetectable in test tubes and two orders of magnitude less in shaken bottles than in unshaken bottles. When these facts are coupled with the inherent statistical advantage of replicating large rather than small experimental units, it is concluded that sampling error in the enumeration of aquatic bacteria in microcosms will be reduced by using numerous, small, violently agitated microcosms with a minimum of subsampling per microcosm.     

Dispersal dynamics of groundwater bacteria

Dispersal of bacteria in saturated, porous soils can be characterized by the partitioning of cells between the aqueous and solid phases, as a result of the physical and chemical nature of the soil and water and cell surface modifications. The purpose of this work is to understand variations in partitioning as a consequence of the nutrient conditions and to use this information in mathematical models to predict the dispersal rate of bacteria in aquifer material. Two different models were used to describe dispersal: an advective-dispersive-sorptive model with a first order kinetic sink term to account for irreversible cell reactions, such as death and sorption; and a two-site reaction model, in which the retardation was assumed to be determined by two types of sites, one characterized by instantaneous equilibrium sorption reactions and the other by kinetic nonequilibrium reactions. Water-saturated sand columns were used as continuous-flow groundwater microcosms to test the models under different nutrient regimes. Two strains of indigenous groundwater bacteria were isolated from aquifer material and labelled with³H-alanine,¹⁴C-pyruvic acid,³H-glucose, and³H-adenosine for different measurements of sorption and dispersal, which were estimated from breakthrough curves. Both experimental data and model variables showed that dispersal of bacteria was a dynamic nonequilibrium process, possibly shaped by two subpopulations, one strongly, even irreversibly, adsorbing to the solid particles, and one with very slow adsorption kinetics. The cell surfaces were modified in response to the growth conditions, which was demonstrated by hydrophobic and electrostatic interaction chromatography. Cell surface hydrophobicity was about eight times higher in groundwater than in eutrophic lake water. The partition coefficient varied between 12.6 in the groundwater and 6.4 in the lake water, indicating the prime importance of hydrophobic binding for attachment in low nutrient conditions. The partitioning was also sensitive to the hydrodynamics of the system and the oxygen supply, as demonstrated by comparison of sorption in agitated test tubes, gently shaken vials, and air-flushed bottles. Sorption kinetics were demonstrated in a continuous flow cell. About 45% of a population was associated with sand particles with a continuous flow of pure groundwater and as little as 20% in lake water. However, more than 50% of the bacteria in the aqueous phase were associated with suspended material of less than 60 μm in diameter. This association may enhance dispersal for example, by size exclusion of the colloidal material in the interstitial pores.     

Microbial growth studies in biodiesel blends

Introduction of biofuels to the fuel matrix poses new questions and challenges. The present study investigates the microbiological stability of biodiesel blends in small scale microcosms. The study presents results from incubations of diesel-biodiesel blends with contaminated inoculation water collected from diesel storage tanks to ensure the presence of relevant fuel degrading bacteria. DAPI and qPCR analyses has subsequently shown an increased bacterial growth and activity in the microcosms containing biodiesel blends as the carbon source compared to those microcosms where neat fossil diesel made up the carbon source. Several anaerobic microorganisms have been identified after incubation. Presence of methanogens, sulfate-reducing bacteria and nitrate reducing bacteria has furthermore been confirmed by chemical analyses, supplemented by observations of methane formation in biodiesel incubations. The findings will contribute to the knowledge base for a safer introduction of biodiesel in the fuel matrix by employment of proper house-keeping and monitoring methods.     

Limulus amoebocyte lysate and direct sampling methods for surveillance of operating nebulizers.

The Limulus amoebocyte lysate test for detection of endotoxin (Pyrogent; Mallinckrodt Chemical Co.) and the Easicult method (Orion Diagnostica) for detection of bacteria were compared with direct dilution sampling, a standardized technique for respiratory therapy surveillance previously developed in our laboratory. Tests of 206 reservoirs of nebulizers were done in three hospitals in Georgia. Forty-five percent of all reservoirs sampled were contaminated. Gram-negative, nonfermentative bacilli were the predominant contaminants. The results of the Limulus test and the Easicult system were in agreement with those of the direct dilution sampling tests approximately 84 and 90% of the time, respectively. Direct dilution of water samples onto blood agar plates was the most sensitive, reliable, and informative method for detecting viable bacteria. The Easicult and Limulus systems were sensitive enough to detect greater than or equal to 10(3) colony-forming units per ml. Positive Limulus tests and negative culture tests, reflecting detection of endotoxin but not of viable gram-negative bacteria, occurred in 20 of 206 (9.7%) instances. Positive cultures and negative Limulus tests were noted in 13 of 206 (6.8%) samplings. The Limulus test is a valuable procedure, for it can detect moderate-to-heavy microbial contamination within 1 h of testing and affords the opportunity to remove contaminated equipment from patients within minutes of a positive test result. These results demonstrate the potential value of the Easicult and Limulus tests for selective surveillance of operating nebulizers.     

Influence of organic matter quality in the cleavage of polymers by marine bacterial communities

The influence of the quality of organic matter on the hydrolysisof polymers by marine bacteria was investigated in microcosmscontaining aggregates created in rolling tanks. Two types ofmicrocosms were analysed: microcosms type M1 from unalteredseawater and microcosms type M2 from phytoplankton cultures.Kinetics of aminopeptidase, -glucosidase and ß-glucosidasewere measured in the ambient water and the aggregates in thetwo types of microcosms. Bacteria attached to aggregates expressedenzymes with K_m values higher than those of the bacteria inthe ambient water for the three hydrolytic activities analysedin both types of microcosms. Attached bacteria showed higherrates of polymer hydrolysis than free-living bacteria only inmicrocosms M2 created from freshly produced phytoplanktonicmaterial, while free-living bacteria were more active than attachedbacteria in the microcosms M1 containing unaltered seawater.The ratio V_max/K_m, which describes the ability of enzymes tocompete at low substrate concentration, shows that free-livingbacteria are more efficient at dealing with low substrate concentrationsin microcosms derived from natural seawater, where the liquidphase may be depleted of utilizable dissolved organic matter,than in the microcosms derived from phytoplankton cultures.Our data suggest that the hydrolytic activities of both attachedand free-living bacteria are significantly influenced by thequality of the aggregates and the consequences of this influenceare discussed.     

In Situ Spatial Patterns of Soil Bacterial Populations,Mapped at Multiple Scales,in an Arable Soil

Very little is known about the spatial organization of soil microbes across scales that are relevant both to microbial function and to field-based processes. The spatial distributions of microbes and microbially mediated activity have a high intrinsic variability. This can present problems when trying to quantify the effects of disturbance, management practices, or climate change on soil microbial systems and attendant function. A spatial sampling regime was implemented in an arable field. Cores of undisturbed soil were sampled from a 3 × 3 × 0.9 m volume of soil (topsoil and subsoil) and a biological thin section, in which the in situ distribution of bacteria could be quantified, prepared from each core. Geostatistical analysis was used to quantify the nature of spatial structure from micrometers to meters and spatial point pattern analysis to test for deviations from complete spatial randomness of mapped bacteria. Spatial structure in the topsoil was only found at the microscale (micrometers), whereas evidence for nested scales of spatial structure was found in the subsoil (at the microscale, and at the centimeter to meter scale). Geostatistical ranges of spatial structure at the micro scale were greater in the topsoil and tended to decrease with depth in the subsoil. Evidence for spatial aggregation in bacteria was stronger in the topsoil and also decreased with depth in the subsoil, though extremely high degrees of aggregation were found at very short distances in the deep subsoil. The data suggest that factors that regulate the distribution of bacteria in the subsoil operate at two scales, in contrast to one scale in the topsoil, and that bacterial patches are larger and more prevalent in the topsoil.     

Citric acid production from imumu Cyperus esculentus and Maize Zea mays

The production of citric acid from imumu Cyperus esculentus and maize Zea mays was carried out using Aspergillus niger. Hydrolysis of the substrates at 97°C produced a higher concentration of reducing sugars than at 40°C. The concentrations of citric acid were higher in unagitated and defatted cultures compared to agitated and undefatted cultures respectively.     

Characterization and identification of numerically abundant culturable bacteria from the anoxic bulk soil of rice paddy microcosms.

Most-probable-number (liquid serial dilution culture) counts were obtained for polysaccharolytic and saccharolytic fermenting bacteria in the anoxic bulk soil of flooded microcosms containing rice plants. The highest viable counts (up to 2.5 x 10(8) cells per g [dry weight] of soil) were obtained by using xylan, pectin, or a mixture of seven mono- and disaccharides as the growth substrate. The total cell count for the soil, as determined by using 4', 6-diamidino-2-phenylindole staining, was 4.8 x 10(8) cells per g (dry weight) of soil. The nine strains isolated from the terminal positive tubes in counting experiments which yielded culturable populations that were equivalent to about 5% or more of the total microscopic count population belonged to the division Verrucomicrobia, the Cytophaga-Flavobacterium-Bacteroides division, clostridial cluster XIVa, clostridial cluster IX, Bacillus spp., and the class Actinobacteria. Isolates originating from the terminal positive tubes of liquid dilution series can be expected to be representatives of species whose populations in the soil are large. None of the isolates had 16S rRNA gene sequences identical to 16S rRNA gene sequences of previously described species for which data are available. Eight of the nine strains isolated fermented sugars to acetate and propionate (and some also fermented sugars to succinate). The closest relatives of these strains (except for the two strains of actinobacteria) were as-yet-uncultivated bacteria detected in the same soil sample by cloning PCR-amplified 16S rRNA genes (U. Hengstmann, K.-J. Chin, P. H. Janssen, and W. Liesack, Appl. Environ. Microbiol. 65:5050-5058, 1999). Twelve other isolates, which originated from most-probable-number counting series indicating that the culturable populations were smaller, were less closely related to cloned 16S rRNA genes.     

A survey of soil microorganisms,with particular reference to the actinomycetes as sources of substances toxic to Heliothis virescens

Cultures of microorganisms isolated from cultivated soils were grown in submerged fermentation in test tubes kept on a rotary shaker at 28°C for 5 days using a fermentation medium composed primarily of soybean flour and dextrose. The beers were harvested and centrifuged, and the supernatants were incorporated at a dilution of 1:10 into artificial diets on which neonate larvae of Heliothis virescens were allowed to feed ad libitum for 7 days. If the beer killed or markedly retarded the development of at least 50% of the test larvae, the culture was regrown in shaken cultures in 500-ml Erlenmeyer flasks and assayed again. If a culture produced toxic beers in both fermentations, it was considered active. Over 2100 soil isolates were tested, of which an estimated 95% were actinomycetes. Slightly over 0.4% of the isolates were active, all of which, probably due to our selection procedure, were actinomycetes.     

A novel method for sampling bacteria on plant root and soil surfaces at the microhabitat scale

This study reports the first method for sampling bacteria at a spatial scale approximating a microhabitat. At the core of this method is the use of tungsten rods with laser-cut tips of known surface area (0.013 mm(2)). Exposed plant root or soil surfaces were viewed with a dissecting microscope and micro-sampling rods were guided to sample sites using a micro-manipulator. Bacteria that adhered to the sampling tips were then recovered for microbiological analyses. The efficiency of this method for removing bacteria from root surfaces was similar to that with which bacteria are recovered from dissected root segments using the conventional technique of washing. However, as the surface area of the micro-sampling tips was known, the new method has the advantage of eliminating inaccuracy in estimates of bacterial densities due to inaccurate estimation of the root or soil surface sampled. When used to investigate spatial distributions of rhizoplane bacteria, the new technique revealed trends that were consistent with those reported with existing methods, while providing access to additional information about community structure at a much smaller spatial scale. The spatial scale of this new method is ca. 1000-times smaller than other sampling methods involving swabbing. This novel technique represents an important methodological step facilitating microbial ecological investigations at a microhabitat scale.     

Evaluation of commercial presence-absence test kits for detection of total coliforms, Escherichia coli, and other indicator bacteria.

Evaluations of several commercial presence-absence (P-A) test kits were performed over a 6-month period in 1990 by using the Ontario Ministry of the Environment (MOE) P-A test for comparison. The general principles of the multiple-tube fermentation technique formed the basis for conducting the product evaluations. Each week, a surface water sample was diluted and inoculated into 25 99-ml dilution blanks for each of three dilutions. The inoculated dilution blanks from each dilution series were randomly sorted into sets of five. Three of these sets were inoculated into the P-A test kits or vice versa, as required. The other two sets were passed through membrane filters, and one set of five membrane filters was placed onto m-Endo agar LES to give replicate total coliform counts and the other set was placed onto m-TEC agar to give replicate fecal coliform results. A statistical analysis of the results was performed by a modified logistic transform method, which provided an improved way to compare binary data obtained from the different test kits. The comparative test results showed that three of the four commercial products tested gave very good levels of recovery and that the fourth commercial product gave only fair levels of recovery when the data were compared with the data from MOE P-A tests and membrane filter tests. P-A bottles showing positive results after 18 h of incubation that were subcultured immediately in ECMUG tubes frequently could be confirmed as containing total coliforms, fecal coliforms, or Escherichia coli after 6 h of incubation; thus, the total incubation time was only 24 h.(ABSTRACT TRUNCATED AT 250 WORDS)     

Impact of protozoan grazing on bacterial community structure in soil microcosms

The influence of grazing by a mixed assemblage of soil protozoa (seven flagellates and one amoeba) on bacterial community structure was studied in soil microcosms amended with a particulate resource (sterile wheat roots) or a soluble resource (a solution of various organic compounds). Sterilized soil was reinoculated with mixed soil bacteria (obtained by filtering and dilution) or with bacteria and protozoa. Denaturing gradient gel electrophoresis (DGGE) of PCR amplifications of 16S rRNA gene fragments, as well as community level physiological profiling (Biolog plates), suggested that the mixed protozoan community had significant effects on the bacterial community structure. Excising and sequencing of bands from the DGGE gels indicated that high-G+C gram-positive bacteria closely related to Arthrobacter spp. were favored by grazing, whereas the excised bands that decreased in intensity were related to gram-negative bacteria. The percentages of intensity found in bands related to high G+C gram positives increased from 4.5 and 12.6% in the ungrazed microcosms amended with roots and nutrient solution, respectively, to 19.3 and 32.9% in the grazed microcosms. Protozoa reduced the average bacterial cell size in microcosms amended with nutrient solution but not in the treatment amended with roots. Hence, size-selective feeding may explain some but not all of the changes in bacterial community structure. Five different protozoan isolates (Acanthamoeba sp., two species of Cercomonas, Thaumatomonas sp., and Spumella sp.) had different effects on the bacterial communities. This suggests that the composition of protozoan communities is important for the effect of protozoan grazing on bacterial communities.     

Effect of tank bromeliad micro-environment on <Emphasis Type="Italic">Aedes aegypti</Emphasis> larval mortality

Many species of bromeliads create an aquatic microcosm among their leaves. Besides their native aquatic fauna, these microcosms can be used by larvae of invasive mosquitoes like Aedes aegypti. We compared the mortality among A. aegypti larvae placed inside tanks of Aechmea fasciata bromeliads with larvae placed inside artificial microcosms and with microcosms with low pH (5.4), which simulate the acidic conditions found inside bromeliad tanks. A. aegypti larvae suffered a significantly higher mortality inside bromeliad tanks compared to larvae in control microcosms, but the mortality inside bromeliads did not differ statistically from that found in artificial microcosms simulating bromeliad acidic conditions. We concluded that bromeliad tanks tend to be a less suitable environment for the development of A. aegypti larvae than artificial containers due to the acidification generated by bromeliad physiology.     

Microbial composition of the activated sludge of Moscow wastewater treatment plants

The contribution of the major technologically important microbial groups (ammonium- and nitrite-oxidizing, phosphate-accumulating, foam-inducing, and anammox bacteria, as well as planctomycetes and methanogenic archaea) was characterized for the aeration tanks of the Moscow wastewater treatment facilities. FISH investigation revealed that aerobic sludge were eubacterial communities; the metabolically active archaea contributed insignificantly. Stage II nitrifying microorganisms and planctomycetes were significant constituents of the bacterial component of activated sludges, with Nitrobacter spp. being the dominant nitrifiers. No metabolically active anammox bacteria were revealed in the sludge from aeration tanks. The sludge from the aeration tanks using different wastewater treatment technologies were found to have differing characteristics. Abundance of the nitrifying and phosphate-accumulating bacteria in the sludge generally correlated with microbial activity in microcosms and with efficiency of nitrogen and phosphorus removal from wastewater. The highest microbial numbers and activity were found in the sludge of the tanks operating according to the technologies developed in the universities of Hannover and Cape Town. The activated sludge from the Novokur’yanovo facilities, where abundant growth of filamentous bacteria resulted in foam formation, exhibited the lowest activity. The group of foaming bacteria included Gordonia spp. and Acinetobacter spp utilizing petroleum and motor oils, Sphaerotilus spp. utilizing unsaturated fatty acids, and Candidatus ‘Microthrix parvicella’. Thus, the data on abundance and composition of metabolically active microorganisms obtained by FISH may be used for the technological control of wastewater treatment.     

Monitoring temporal and spatial variation in rhizosphere bacterial population diversity: A community approach for the improved selection of rhizosphere competent bacteria

The potential for developing a reliable strategy for selecting rhizosphere competent bacteria, based on an improved understanding of the community diversity and population dynamics of fluorescent pseudomonads, was investigated. Isolates from a collection of over 690 fluorescent pseudomonads, obtained from sugar beet and wheat plants grown in field soils in laboratory microcosms, were genotypically and phenotypically characterised. RFLP rRNA analysis (ribotyping) revealed that the sampled population was composed of 385 related but distinct ribotypes. Most ribotypes were isolated only once and represented a transient colonising population. However, representatives of 26 ribotypes were detected more often, of which five were isolated from rhizosphere soils sampled 7 months after the first sampling. Comparative phenotypic analysis of isolates (motility, antibiotic resistance and production, adherence, fatty acid composition, substrate utilisation patterns) demonstrated that the ability to utilise organic acids as carbon sources correlated with rhizosphere competence. Single inoculum and competitive colonisation studies in planted microcosms confirmed rhizosphere competence, but also demonstrated synergistic interactions. The colonisation ability and population densities of transient strains were significantly increased when co-inoculated with rhizosphere competent isolates. These data demonstrate potential cross-feeding and combined niche exploitation, rather than direct competition, confirming the multi-factorial nature of rhizosphere competence in diverse fluorescent pseudomonad communities. They also highlight the need to consider the use of mixed inocula for plant growth promotion and the systematic selection of strains for effective biotechnological exploitation.     

Growth and molecular characterization of dental plaque microcosms

AIMS: (i) To compare the effects of feeding protocols upon the composition and stability of dental plaque microcosms formed in constant-depth film fermenters (CDFF). (ii) To evaluate the utility of denaturing gradient gel electrophoresis (DGGE) and culture methodologies for the investigation of such models. METHODS AND RESULTS: Microcosms were established anaerobically in the CDFFs from freshly collected saliva. These were fed either with artificial saliva alone (famine) or combined with discontinuous feeding (feast-famine). Culture and 16s rDNA sequencing indicated that supplemental feeding gave ca. 2 log increases in Lactobacillus rhamnosus and Prevotella buccae. Feast-famine microcosms were then further characterized by DGGE using primers specific for the V2-V3 region of eubacterial rDNA. These gave single major bands with pure cultures (eight species) and resolved all strains apart from Lact. rhamnosus and Actinomyces naeslundii. Whilst culture with selective media indicated a degree of stability and reproducibility between replicate microcosms, DGGE showed a considerable degree of variability that related to several putatively uncultured bacteria. CONCLUSIONS: Feast-famine regimes altered community composition. DGGE analyses identified putatively unculturable species and demonstrated variability between replicate fermenters. SIGNIFICANCE AND IMPACT OF THE STUDY: This study demonstrates the utility of DGGE for the analysis of dental plaque, especially with respect to unculturable bacteria. Results question the assumptions of reproducibility of plaque microcosms established in non-replicated CDFFs made on the basis of selective media. Feeding regimes, particularly those involving complex nutrients, will dramatically affect population dynamics.     

Some special problems in the determination of viable counts of groundwater microorganisms

Factors affecting viable cell counts in groundwater or sediments were studied with samples from the Segeberg Forest test area in northern Germany. There was very little variation in results with the season (April, August, November) or depth of sampling; generally there were 10³–10⁴ aerobic cells per ml or g sediment. Long incubation times resulted in higher cell counts; groundwater samples required 4–5 weeks, and sediment extracts had to be cultured for 7 weeks. Total cell counts in sediment were 10²–10⁴ cell/g higher than viable cell counts of aerobes. This was explained partly by the additional presence of anaerobes and partly by the observation that some morphotypes may not have grown under our conditions. Viable cell counts were not influenced by cell extraction from the sediment with either Na-pyrophosphate or groundwater extracts. However, iron-precipitating or manganese-oxidizing bacteria were better extracted with sterile groundwater. The microflora of wells was more numerous than that of the free aquifer; consequently it was better to pump off all well water before aquifer water was sampled. The diameter of the well was also important; thinner tubes had higher cell counts than those with wider diameter. For sampling, wells should be at least 1 year old, since young wells contain higher numbers of microorganisms due to underground disturbances from the drilling. Turbid water samples could be clarified by filtration, but this reduced the viable counts by 1–2 orders of magnitude. Two different media inoculated with a sample dilution resulted in the same cell counts, but their microbial diversity was different. Storage of groundwater samples before processing resulted in up to 17-fold increases in cell counts and loss of diversity in the first 24 hours. Cell numbers decreased slowly during longer storage.     

Study of the bacterial flora of a non-carbonated natural mineral water

Natural mineral water from a UK spring was monitored at various stages after it was pumped from the ground, through to bottling and during shelf life before consumption. Samples were collected in commercial PVC bottles, in PVC bottles previously sterilized and hand-filled and in glass bottles. The bacterial flora was counted on plate count agar (PCA) and on PCA diluted 10 times (PCA/10). The predominant bacteria were identified to genus level. Growth rates and nutrient types of isolates were determined by the nutrient-tolerance test (NT). The plate counts at the prebottling stage were low. During storage larger numbers of bacteria grew in glass than PVC bottles; the largest number grew in PVC bottles filled by hand. Most of the pigmented bacteria isolated were oligocarbotolerant.     

Potential sources of error during virus thermal inactivation.

A review of virus thermal inactivation data published in the literature demonstrated variations in reported virus resistance. Examination of the methods used indicated that numerous studies were made by heat processing virus suspensions in test tubes. Duplication of some of the methods using milk suspensions of poliovirus 1 showed virus persistence after heating as a result of uneven temperature distribution inside the test tubes. Unless the containers (preferably sealed ampoules or capillary tubes) are completely submerged in the water bath and agitated vigorously, apparent virus persistence may be encountered.     

Potential sources of error during virus thermal inactivation.

A review of virus thermal inactivation data published in the literature demonstrated variations in reported virus resistance. Examination of the methods used indicated that numerous studies were made by heat processing virus suspensions in test tubes. Duplication of some of the methods using milk suspensions of poliovirus 1 showed virus persistence after heating as a result of uneven temperature distribution inside the test tubes. Unless the containers (preferably sealed ampoules or capillary tubes) are completely submerged in the water bath and agitated vigorously, apparent virus persistence may be encountered.