Microtechnique for most-probable-number analysis

MicroMPN: methods and software for high-throughput screening of microbe suppression in mixed populations

Screening assays are used to test if one or more microbes suppress a pathogen of interest. In the presence of more than one microbe, the screening method must be able to accurately distinguish viable pathogen cells from non-viable and non-target microbes in a sample. Current screening methods are time-consuming and require special reagents to detect viability in mixed microbial communities. Screening assays performed using soil or other complex matrices present additional challenges for screening. Here, we develop an experimental workflow based on the most probable number (MPN) assay for testing the ability of synthetic microbial communities to suppress a soil-borne pathogen. Our approach, fluorMPN, uses a fluorescently labeled pathogen and microplate format to enable high-throughput comparative screening. In parallel, we developed a command-line tool, MicroMPN, which significantly reduces the complexity of calculating MPN values from microplates. We compared the performance of the fluorMPN assay with spotting on agar and found that both methods produced strongly correlated counts of equal precision. The suppressive effect of synthetic communities on the pathogen was equally recoverable by both methods. The application of this workflow for discriminating which communities lead to pathogen reduction helps narrow down candidates for additional characterization. Together, the resources offered here are meant to facilitate and simplify the application of MPN-based assays for comparative screening projects.IMPORTANCEWe created a unified set of software and laboratory protocols for screening microbe libraries to assess the suppression of a pathogen in a mixed microbial community. Existing methods of fluorescent labeling were combined with the most probable number (MPN) assay in a microplate format to enumerate the reduction of a pathogenic soil microbe from complex soil matrices. This work provides a fluorescent expression vector available from Addgene, step-by-step laboratory protocols hosted by protocols.io, and MicroMPN, a command-line software for processing plate reader outputs. MicroMPN simplifies MPN estimation from 96- and 384-well microplates. The microplate screening assay is amenable to robotic automation with standard liquid handling robots, further reducing the hands-on processing time. This tool was designed to evaluate synthetic microbial communities for use as microbial inoculates or probiotics. The fluorMPN method is also useful for screening chemical and antimicrobial libraries for pathogen suppression in complex bacterial communities like soil.

A novel procedure for CFU plating and counting

We present a novel method to automate plating for the Colony Forming Unit (CFU) counting procedure. The apparatus we developed for the application of this method is based on motorized stages and a syringe in order to spread fine drops of a liquid containing a solution of interest on a plate without direct contact with the surface. The apparatus can be used in two different modes. In the the first method which follows the same principle as the classical CFU count, fine drops of liquid are deposited homogeneously on an agar plate and microorganisms are allowed to form colonies. In the second, novel method that we call P₀, isolated drops of the order of 10 μL containing both the microbes and the nutrient medium are deposited directly on a regular grid on a hard surface (plastic or glass); after incubation, drops that show no sign of growth inside are used to determine the microbes concentration. This new method removes the need for preparing agar surfaces and allows for easy disposal of waste and reuse of consumables. The apparatus is simple to build and use, the plating is fast and the CFU count in both type of plating is extremely reproducible and robust.

Molecular characterization and antimicrobial susceptibility profiles of Thai Mycoplasma synoviae isolates

Mycoplasma synoviae (MS) infection is mainly controlled by pathogen-free flocks' maintenance, medication in infected flocks, and vaccination in high-risk flocks. The effective control strategy requires convenient approach for detecting and differentiating MS strains and reliable drug susceptible evidence for deciding on reasonable antimicrobial usage. This study aimed to characterize the partial vlhA gene of nine Thai MS isolates circulated in chickens in 2020, to verify the PCR-RFLP assay for strain differentiation, and to determine the eight antimicrobial susceptibility profiles using microbroth dilution method. Based on sequence analysis of the partial vlhA gene, Thai MS isolates in 2020 were classified as types E and L with 19 and 35 amino acid lengths, respectively. The developed PCR-RFLP assay could detect and differentiate vaccine and Thai field strains. Most Thai MS isolates in this study were susceptible to tylosin, tylvalosin, tiamulin, doxycycline, oxytetracycline, tilmicosin, and lincomycin-spectinomycin at MIC₅₀ values of 0.0391, 0.0098, 0.0781, 0.1563, 0.1563, 0.625 and 0.625 μg/mL, respectively; and resistance to enrofloxacin at MIC₅₀ value of 10 μg/mL. In conclusion, this study revealed diagnostic assays for differentiating MS strains and the antimicrobial susceptibility profiles of Thai MS, which are necessary to design suitable MS control procedures for poultry flocks.

Supercharged MPNs? Automated Determination of High-Throughput Most Probable Number (htMPN) Using Chip-Based 3D Digital PCR

Surface plating on agar and most probable number (MPN) are the standard methods for determining bacterial viability but both have limitations. Here we present a novel cell count method, high-throughput MPN (htMPN), that uses a chip-based digital PCR instrument to accelerate and to improve the quantification of viable or sublethally injured cells. This method tracks growth of up to 20,000 individual bacterial cells on a single chip. Single cells were grown in the individual wells of the chip at their optimal temperature until the cell density was high enough to detect the fluorescent signal with cell-permeant or cell-impermeant DNA-intercalating fluorescent dyes. This method based on microfluidic devices implemented in digital PCR equipment was equivalent to surface plating in determining cell counts of Escherichia coli, Salmonella enterica serovar Typhimurium, Fructilactobacillus sanfranciscensis, Pseudomonas putida, and vegetative cells but not spores of Bacillus subtilis. Viable E. coli could be enumerated within 7 h. Culture of strict aerobes was restricted to strains that are capable of nitrate respiration; organisms requiring complex media that also contain double-stranded DNA were detected after treatment of growth media with DNase before inoculation. Our approach not only monitors the frequency distribution of bacterial growth and determines cell counts with high reliability but also detected heat-injured cells of S. Typhimurium that escaped detection by the surface plating. Overall, the method accelerates detection of viable bacterial cells, facilitates automation, and offers new possibilities for the analysis of individual bacterial cells. IMPORTANCE htMPN uses chip-based fluorescence acquisition and is a simple and compact tool for automatic viable cell enumeration with applications in microbiological research. This method applies to a wide range of anaerobic or facultative anaerobic species and improves accuracy by reducing the number of pipetting steps. In addition, the method offers an additional tool for single-cell microbiology. The single cell time-to-detection times have been used as an important criterion for the physiological state of bacterial cells after sublethal stress, and htMPNs support the acquisition of such data with an unprecedented number of cells. In particular, htMPN provides an anaerobic environment and enables a long incubation time to increase the recovery rate of sublethally injured cells. Given its reproducibility and reliability, our approach can potentially be applied to quantify viable cells in samples from environmental, clinical, or food samples to reduce the risk of underestimation of the number of viable bacterial cells.

Self-reinoculation with fecal flora changes microbiota density and composition leading to an altered bile-acid profile in the mouse small intestine

BACKGROUND

The upper gastrointestinal tract plays a prominent role in human physiology as the primary site for enzymatic digestion and nutrient absorption, immune sampling, and drug uptake. Alterations to the small intestine microbiome have been implicated in various human diseases, such as non-alcoholic steatohepatitis and inflammatory bowel conditions. Yet, the physiological and functional roles of the small intestine microbiota in humans remain poorly characterized because of the complexities associated with its sampling. Rodent models are used extensively in microbiome research and enable the spatial, temporal, compositional, and functional interrogation of the gastrointestinal microbiota and its effects on the host physiology and disease phenotype. Classical, culture-based studies have documented that fecal microbial self-reinoculation (via coprophagy) affects the composition and abundance of microbes in the murine proximal gastrointestinal tract. This pervasive self-reinoculation behavior could be a particularly relevant study factor when investigating small intestine microbiota. Modern microbiome studies either do not take self-reinoculation into account, or assume that approaches such as single housing mice or housing on wire mesh floors eliminate it. These assumptions have not been rigorously tested with modern tools. Here, we used quantitative 16S rRNA gene amplicon sequencing, quantitative microbial functional gene content inference, and metabolomic analyses of bile acids to evaluate the effects of self-reinoculation on microbial loads, composition, and function in the murine upper gastrointestinal tract.

RESULTS

In coprophagic mice, continuous self-exposure to the fecal flora had substantial quantitative and qualitative effects on the upper gastrointestinal microbiome. These differences in microbial abundance and community composition were associated with an altered profile of the small intestine bile acid pool, and, importantly, could not be inferred from analyzing large intestine or stool samples. Overall, the patterns observed in the small intestine of non-coprophagic mice (reduced total microbial load, low abundance of anaerobic microbiota, and bile acids predominantly in the conjugated form) resemble those typically seen in the human small intestine.

CONCLUSIONS

Future studies need to take self-reinoculation into account when using mouse models to evaluate gastrointestinal microbial colonization and function in relation to xenobiotic transformation and pharmacokinetics or in the context of physiological states and diseases linked to small intestine microbiome and to small intestine dysbiosis. Video abstract.

Sources and transformations of anthropogenic nitrogen in the highly disturbed Huai River Basin, Eastern China

Due to serious nitrogen pollution in the Huai River, Eastern China, nitrogenous concentrations and dual stable isotopes (δ¹⁵N and δ¹⁸O) were measured to ascertain the sources and transformation of nitrogen in the Shaying River, the largest and most polluted tributary of the Huai River during the summer and winter seasons. Total nitrogen (TN), NO₃^-, and NH₄⁺ were significantly higher in winter, with values of 7.84 ± 3.44 mg L^-1, 2.31 ± 0.81 mg L^-1, and 3.00 ± 2.24 mg L^-1, respectively, while the highest nitrogen compounds occurred in the Jialu River, one of the tributaries of the Shaying River, in both summer and winter. Isotope characteristics of nitrate reveal that manure and sewage were the principal nitrate sources in both summer (62.44 ± 19.66%) and winter (67.33 ± 15.45%), followed by soil organic nitrogen, with 24.94 ± 15.52% in summer and 26.33 ± 9.45% in winter. Values of δ¹⁵N-suspended particulate nitrogen (SPN) ranged from 0.78 to 13.51%, revealing that point source from industrial and domestic sewage accounted for the largest input to SPN at most sites, whereas soil organic nitrogen and agricultural fertilizers were found in the Jialu River in both sampling periods. Point sources from septic/manure and household waste were the main contributors to ammonium in most river water samples in both summer and winter; most wastewater discharged into the river was untreated, which was one of the main reasons for the high level of ammonium in winter. Nitrogen pollution and the dams had an effect on N transformation in the river. Significant assimilation of NH₄⁺ and aerobic denitrification competed for NH₄⁺, resulting in the weakness of nitrification in the summer. Denitrification was also an important process of nitrate removal during the summer, whereas nitrification was a key N transformation process in the river in the winter time. To reduce nitrogen pollution and improve water quality, greater effort should be focused on the management of sources from urban input as well as on the improvement in sewage treatment.

Land-use influences phosphatase gene microdiversity in soils

Phosphorus cycling exerts significant influence upon soil fertility and productivity - processes largely controlled by microbial activity. We adopted phenotypic and metagenomic approaches to investigate phosphatase genes within soils. Microbial communities in bare fallowed soil showed a marked capacity to utilise phytate for growth compared with arable or grassland soil communities. Bare fallowed soil contained lowest concentrations of orthophosphate. Analysis of metagenomes indicated phoA, phoD and phoX, and histidine acid and cysteine phytase genes were most abundant in grassland soil which contained the greatest amount of NaOH-EDTA extractable orthophosphate. Beta-propeller phytase genes were most abundant in bare fallowed soil. Phylogenetic analysis of metagenome sequences indicated the phenotypic shift observed in the capacity to mineralise phytate in bare fallow soil was accompanied by an increase in phoD, phoX and beta-propeller phytase genes coding for exoenzymes. However, there was a remarkable degree of genetic similarity across the soils despite the differences in land-use. Predicted extracellular ecotypes were distributed across a greater range of soil structure than predicted intracellular ecotypes, suggesting that microbial communities subject to the dual stresses of low nutrient availability and reduced access to organic material in bare fallowed soils rely upon the action of exoenzymes.

Potential for Sulfate Reduction in Mangrove Forest Soils: Comparison between Two Dominant Species of the Americas

Avicennia and Rhizophora are globally occurring mangrove genera with different traits that place them in different parts of the intertidal zone. It is generally accepted that the oxidizing capacity of Avicennia roots is larger than that of Rhizophora roots, which initiates more reduced conditions in the soil below the latter genus. We hypothesize that the more reduced conditions beneath Rhizophora stands lead to more active sulfate-reducing microbial communities compared to Avicennia stands. To test this hypothesis, we measured sulfate reduction traits in soil samples collected from neighboring Avicennia germinans and Rhizophora mangle stands at three different locations in southern Florida. The traits measured were sulfate reduction rates (SRR) in flow-through reactors containing undisturbed soil layers in the absence and presence of easily degradable carbon compounds, copy numbers of the dsrB gene, which is specific for sulfate-reducing microorganisms, and numbers of sulfate-reducing cells that are able to grow in liquid medium on a mixture of acetate, propionate and lactate as electron donors. At the tidal locations Port of the Islands and South Hutchinson Islands, steady state SRR, dsrB gene copy numbers and numbers of culturable cells were higher at the A. germinans than at the R. mangle stands, although not significantly for the numbers at Port of the Islands. At the non-tidal location North Hutchinson Island, results are mixed with respect to these sulfate reduction traits. At all locations, the fraction of culturable cells were significantly higher at the R. mangle than at the A. germinans stands. The dynamics of the initial SRR implied a more in situ active sulfate-reducing community at the intertidal R. mangle stands. It was concluded that in agreement with our hypothesis R. mangle stands accommodate a more active sulfate-reducing community than A. germinans stands, but only at the tidal locations. The differences between R. mangle and A. germinans stands were absent at the non-tidal, impounded location.

Investigation of Archaeal and Bacterial community structure of five different small drinking water networks with special regard to the nitrifying microorganisms

Total microbial community structure, and particularly nitrifying communities inhabiting five different small drinking water networks characterized with different water physical and chemical parameters was investigated, using cultivation-based methods and sequence aided Terminal Restriction Fragment Length Polymorphism (T-RFLP) analysis. Ammonium ion, originated from well water, was only partially oxidized via nitrite to nitrate in the drinking water distribution systems. Nitrification occurred at low ammonium ion concentration (27-46μM), relatively high pH (7.6-8.2) and over a wide range of dissolved oxygen concentrations (0.4-9.0mgL(-1)). The nitrifying communities of the distribution systems were characterized by variable most probable numbers (2×10(2)-7.1×10(4) MPN L(-1)) and probably originated from the non-treated well water. The sequence aided T-RFLP method revealed that ammonia-oxidizing microorganisms and nitrite-oxidizing Bacteria (Nitrosomonas oligotropha, Nitrosopumilus maritimus, and Nitrospira moscoviensis, 'Candidatus Nitrospira defluvii') were present in different ratios in the total microbial communities of the distinct parts of the water network systems. The nitrate generated by nitrification was partly utilized by nitrate-reducing (and denitrifying) Bacteria, present in low MPN and characterized by sequence aided T-RFLP as Comamonas sp. and Pseudomonas spp. Different environmental factors, like pH, chemical oxygen demand, calculated total inorganic nitrogen content (moreover nitrite and nitrate concentration), temperature had important effect on the total bacterial and archaeal community distribution.

Potential Activity, Size, and Structure of Sulfate-Reducing Microbial Communities in an Exposed, Grazed and a Sheltered, Non-Grazed Mangrove Stand at the Red Sea Coast

After oxygen, sulfate is the most important oxidant for the oxidation of organic matter in mangrove forest soils. As sulfate reducers are poor competitors for common electron donors, their relative success depends mostly on the surplus of carbon that is left by aerobic organisms due to oxygen depletion. We therefore hypothesized that sulfate-cycling in mangrove soils is influenced by the size of net primary production, and hence negatively affected by mangrove degradation and exploitation, as well as by carbon-exporting waves. To test this, we compared quantitative and qualitative traits of sulfate-reducing communities in two Saudi-Arabian mangrove stands near Jeddah, where co-occurring differences in camel-grazing pressure and tidal exposure led to a markedly different stand height and hence primary production. Potential sulfate reduction rates measured in anoxic flow-through reactors in the absence and presence of additional carbon sources were significantly higher in the samples from the non-grazed site. Near the surface (0–2 cm depth), numbers of dsrB gene copies and culturable cells also tended to be higher in the non-grazed sites, while these differences were not detected in the sub-surface (4–6 cm depth). It was concluded that sulfate-reducing microbes at the surface were indeed repressed at the low-productive site as could be expected from our hypothesis. At both sites, sulfate reduction rates as well as numbers of the dsrB gene copies and viable cells increased with depth suggesting repression of sulfate reduction near the surface in both irrespective of production level. Additionally, sequence analysis of DNA bands obtained from DGGE gels based on the dsrB gene, showed a clear difference in dominance of sulfate-reducing genera belonging to the Deltaproteobacteria and the Firmicutes between sampling sites and depths.

Cell Based Drug Delivery: Micrococcus luteus Loaded Neutrophils as Chlorhexidine Delivery Vehicles in a Mouse Model of Liver Abscesses in Cattle

The recent WHO report on antibiotic resistances shows a dramatic increase of microbial resistance against antibiotics. With only a few new antibiotics in the pipeline, a different drug delivery approach is urgently needed. We have obtained evidence demonstrating the effectiveness of a cell based drug delivery system that utilizes the innate immune system as targeting carrier for antibacterial drugs. In this study we show the efficient loading of neutrophil granulocytes with chlorhexidine and the complete killing of E. coli as well as Fusobacterium necrophorum in in-vitro studies. Fusobacterium necrophorum causes hepatic abscesses in cattle fed high grain diets. We also show in a mouse model that this delivery system targets infections of F. necrophorum in the liver and reduces the bacterial burden by an order of magnitude from approximately 2•106 to 1•105.

Endospore-enriched sequencing approach reveals unprecedented diversity of Firmicutes in sediments

We present a method for the physical isolation of endospores from environmental samples allowing the specific targeting of endospore-forming bacteria for sequencing (endospore-enriched community). The efficiency of the method was tested on lake sediment samples. After 16S rRNA gene amplicon sequencing, the composition in the endospore-enriched community was compared with the community from untreated control samples (whole community). In the whole community, Firmicutes had a relative abundance of 8% and 19% in the two different lake sediments. In contrast, in the endospore-enriched community, Firmicutes abundance increased to 90.6% and 83.9%, respectively, confirming the efficiency of the endospore enrichment. The relative abundance of other microbial groups that form spore-like resisting states (i.e. actinobacteria, cyanobacteria and myxococcales) was below 2% in the endospore-enriched community, indicating that the method is adapted to true endospores. Representatives from two out of the three known classes of Firmicutes (Bacilli and Clostridia) were detected and supposedly asporogenic groups (e.g. Ethanoligenes and Trichococcus) could be detected. The method presented here is a leap forward for ecological studies of endospore-forming Firmicutes. It can be applied to other types of samples in order to reveal the diversity and metabolic potential of this bacterial group in the environment.

Methane oxidation and abundance of methane oxidizers in tropical agricultural soil (vertisol) in response to CuO and ZnO nanoparticles contamination

There is worldwide concern over the increase use of nanoparticles (NPs) and their ecotoxicological effect. It is not known if the annual production of tons of industrial nanoparticles (NPs) has the potential to impact terrestrial microbial communities, which are so necessary for ecosystem functioning. Here, we have examined the consequences of adding the NPs particularly the metal oxide (CuO, ZnO) on CH4 oxidation activity in vertisol and the abundance of heterotrophs, methane oxidizers, and ammonium oxidizers. Soil samples collected from the agricultural field located at Madhya Pradesh, India, were incubated with either CuO and ZnO NPs or ionic heavy metals (CuCl2, ZnCl2) separately at 0, 10, and 20 μg g(-1) soil. CH4 oxidation activity in the soil samples was estimated at 60 and 100 % moisture holding capacity (MHC) in order to link soil moisture regime with impact of NPs. NPs amended to soil were highly toxic for the microbial-mediated CH4 oxidation, compared with the ionic form. The trend of inhibition was Zn 20 > Zn 10 > Cu 20 > Cu 10. NPs delayed the lag phase of CH4 oxidation to a maximum of 4-fold and also decreased the apparent rate constant k up to 50 % over control. ANOVA and Pearson correlation analysis (α = 0.01) revealed significant impact of NPs on the CH4 oxidation activity and microbial abundance (p < 0.0001, and high F statistics). Principal component analysis (PCA) revealed that PC1 (metal concentration) rendered 76.06 % of the total variance, while 18.17 % of variance accounted by second component (MHC). Biplot indicated negative impact of NPs on CH4 oxidation and microbial abundance. Our result also confirmed that higher soil moisture regime alleviates toxicity of NPs and opens new avenues of research to manage ecotoxicity and environmental hazard of NPs.

Structural and functional response of methane-consuming microbial communities to different flooding regimes in riparian soils

Climate change will lead to more extreme precipitation and associated increase of flooding events of soils. This can turn these soils from a sink into a source of atmospheric methane. The latter will depend on the balance of microbial methane production and oxidation. In the present study, the structural and functional response of methane oxidizing microbial communities was investigated in a riparian flooding gradient. Four sites differing in flooding frequency were sampled and soil-physico-chemistry as well as methane oxidizing activities, numbers and community composition were assessed. Next to this, the active community members were determined by stable isotope probing of lipids. Methane consumption as well as population size distinctly increased with flooding frequency. All methane consumption parameters (activity, numbers, lipids) correlated with soil moisture, organic matter content, and conductivity. Methane oxidizing bacteria were present and activated quickly even in seldom flooded soils. However, the active species comprised only a few representatives belonging to the genera Methylobacter, Methylosarcina, and Methylocystis, the latter being active only in permanently or regularly flooded soils.

This study demonstrates that soils exposed to irregular flooding harbor a very responsive methane oxidizing community that has the potential to mitigate methane produced in these soils. The number of active species is limited and dominated by one methane oxidizing lineage. Knowledge on the characteristics of these microbes is necessary to assess the effects of flooding of soils and subsequent methane cycling therein.

Fate of NO and NH in the treatment of eutrophic water using the floating macrophyte

Use of the floating aquatic macrophyte, , to improve eutrophic water quality is practiced on a large scale in China. Limited information is available on the relative importance of the biological NO or NH removal process during the treatment of eutrophic water using . To investigate the key process responsible for the removal of NO and NH, N-NO (9.98 atom % [at.%] N) or N-NH (10.08 at.% N) was added to obtain eutrophic water with or without the cultivation of . In the unplanted water, considerable proportions of the added N-NO (27.13 ± 4.87%) or N-NH (42.08 ± 7.22%) were assimilated by the developed algae. The growth of controlled algae development in the planted water. Furthermore, the cultivation of stimulated gaseous loss of N by microbial denitrification (8.61 ± 1.70% NO-N loss from N-NO-labeled water). Apart from N loss by denitrification, considerable proportions of the added N-NO (62.01 ± 6.93%) or N-NH (76.76 ± 6.21%) were assimilated into the macrophyte N pools. The fine root detritus of contained a proportion of N (4.37 ± 1.39% in NO-labeled water, 2.03 ± 0.52% in NH-labeled water) that will be returned to the water after decomposition. In addition to N loss via NO emission, an unaccounted proportion of N could be mainly due to gaseous loss as N by denitrification (25.00% in N-NO-labeled water with Eichhornia crassipes)

Nitrification and potential control mechanisms in simulated premises plumbing

Indigenous drinking water organisms were used to establish nitrification in glass reactors containing copper or polyvinyl chloride (PVC) surfaces. The reactors were fed soil-derived humics as the organic carbon source and ammonium sulfate as the nitrogen source in biologically treated tap water. Water in the reactors was stagnant for 8 h and then flowed for 5 min to simulate conditions in household plumbing. Following the establishment of complete nitrification (conversion of ammonia to nitrate) in both reactor types, various inhibitors of nitrification were tested followed by a period where recovery of nitrification was observed. In one PVC reactor, copper was gradually introduced up to 1.3 ppm. To ensure that most of the copper was in the ionic form, the pH of the influent was then gradually lowered to 6.6. No significant change in nitrification was observed in the presence of copper. Chlorite was introduced into copper and PVC reactors at doses increasing from 0.2 ppm to 20 ppm. There was limited effect on the PVC system and inhibition in the copper reactor only at 20 ppm. Chloramine was tested at chlorine to ammonia ratios ranging from 0.5:1 to 5:1. Nitrification activity was impacted significantly at a 5:1 ratio and ultimately stopped, with the fastest response being in the copper system. Whenever a control mechanism was tested, there was increased release of copper from the reactors with copper coupons. In all cases, nitrification recovered when inhibitors were removed but the rates of recovery differed depending on the treatment method and coupon surface.

Activity and Distribution of Methane-Oxidizing Bacteria in Flooded Rice Soil Microcosms and in Rice Plants (Oryza sativa)

The activity and distribution of CH(inf4)-oxidizing bacteria (MOB) in flooded rice (Oryza sativa) soil microcosms was investigated. CH(inf4) oxidation was shown to occur in undisturbed microcosms by using (sup14)CH(inf4), and model calculations indicated that almost 90% of the oxidation measured had taken place at a depth where only roots could provide the O(inf2) necessary. Slurry from soil planted with rice had an apparent K(infm) for CH(inf4) of 4 (mu)M and a V(infmax) of 0.1 (mu)mol g (dry weight)(sup-1) h(sup-1). At a depth of 1 to 2 cm, there was no significant difference (P > 0.05) in numbers of MOB between soil from planted and nonplanted microcosms (mean, 7.7 x 10(sup5) g [fresh weight](sup-1)). Thus, the densely rooted soil at 1 to 2 cm deep did not represent rhizospheric soil with respect to the number of MOB. A significantly increased number of MOB was found only in soil immediately around the roots (1.2 x 10(sup6) g [fresh weight](sup-1)), corresponding to a layer of 0.1 to 0.2 mm. Plant-associated CH(inf4) oxidation was shown in a double chamber with carefully washed intact rice plants. Up to 90% of the CH(inf4) supplied to the root compartment was oxidized in the plants. CH(inf4) oxidation on isolated roots was higher and had a larger variability than that in soil slurries. Roots had an apparent K(infm) for CH(inf4) of 6 (mu)M and a V(infmax) of 5 (mu)mol g (dry weight)(sup-1) h(sup-1). The average number of MOB in homogenized roots was larger than on the rhizoplane and increased with plant age. MOB also were found in surface-sterilized roots and basal culms, indicating the ability of these bacteria to colonize the interior of roots and culms.

Coexisting bacterial populations responsible for multiphasic mineralization kinetics in soil

Experiments were conducted to study populations of indigenous microorganisms capable of mineralizing 2,4-dinitrophenol (DNP) in two soils. Previous kinetic analyses indicated the presence of two coexisting populations of DNP-mineralizing microorganisms in a forest soil (soil 1). Studies in which eucaryotic and procaryotic inhibitors were added to this soil indicated that both populations were bacterial. Most-probable-number counts with media containing different concentrations of DNP indicated that more bacteria could mineralize low concentrations of DNP than could metabolize high concentrations of it. Enrichments with varying concentrations of DNP and various combinations of inhibitors consistently resulted in the isolation of the same two species of bacteria from soil 1. This soil contained a large number and variety of fungi, but no fungi capable of mineralizing DNP were isolated. The two bacterial isolates were identified as a Janthinobacterium sp. and a Rhodococcus sp. The Janthinobacterium sp. had a low mu(max) and a low K(m) for DNP mineralization, whereas the Rhodococcus sp. had much higher values for both parameters. These differences between the two species of bacteria were similar to differences seen when soil was incubated with different concentrations of DNP. Values for mu(max) from soil incubations were similar to mu(max) values obtained in pure culture studies. In contrast, K(s) and K(m) values showed greater variation between soil and pure culture studies. The results of this study help to confirm predictions that two physiologically distinct bacterial populations are responsible for the multiphasic mineralization kinetics observed in the soil studied.

Competition for Ammonium between Nitrifying and Heterotrophic Bacteria in Continuously Percolated Soil Columns

Although the absence of nitrate formation in grassland soils rich in organic matter has often been reported, low numbers of nitrifying bacteria are still found in these soils. To obtain more insight into these observations, we studied the competition for limiting amounts of ammonium between the chemolithotrophic ammonium-oxidizing species Nitrosomonas europaea and the heterotrophic species Arthrobacter globiformis in the presence of Nitrobacter winogradskyi with soil columns containing calcareous sandy soil. The soil columns were percolated continuously at a dilution rate of 0.007 h, based on liquid volumes, with medium containing 5 mM ammonium and different amounts of glucose ranging from 0 to 12 mM.A. globiformis was the most competitive organism for limiting amounts of ammonium. The numbers of N. europaea and N. winogradskyi cells were lower at higher glucose concentrations, and the potential ammonium-oxidizing activities in the uppermost 3 cm of the soil columns were nonexistent when at least 10 mM glucose was present in the reservoir, although 10 nitrifying cells per g of dry soil were still present. This result demonstrated that there was no correlation between the numbers of nitrifying bacteria and their activities. The numbers and activities of N. winogradskyi cells decreased less than those of N. europaea cells in all layers of the soil columns, probably because of heterotrophic growth of the nitrite-oxidizing bacteria on organic substrates excreted by the heterotrophic bacteria or because of nitrate reduction at reduced oxygen concentrations by the nitrite-oxidizing bacteria. Our conclusion was that the nitrifying bacteria were less competitive than the heterotrophic bacteria for ammonium in soil columns but that they survived as viable inactive cells. Inactive nitrifying bacteria may also be found in the rhizosphere of grassland plants, which is rich in organic carbon. They are possibly reactivated during periods of net mineralization.

Effects of Grazing by Flagellates on Competition for Ammonium between Nitrifying and Heterotrophic Bacteria in Chemostats

The enhanced mineralization of organic nitrogen by bacteriophagous protozoa is thought to favor the nitrification process in soils, in which nitrifying bacteria have to compete with heterotrophic bacteria for the available ammonium. To obtain more insight into this process, the influence of grazing by the bacteriovorous flagellate Adriamonas peritocrescens on the competition for limiting amounts of ammonium between the ammonium-oxidizing species Nitrosomonas europaea and the heterotrophic species Arthrobacter globiformis was studied in the presence of Nitrobacter winogradskyi in continuous cultures at dilution rates of 0.004 and 0.01 h. The ammonium concentration in the reservoir was maintained at 2 mM, whereas the glucose concentration was increased stepwise from 0 to 7 mM. A. globiformis won the competition for limiting amounts of ammonium when the glucose concentration in the reservoirs increased, in agreement with previously described experiments in which the flagellates were not included. The numbers of nitrifying bacteria decreased as the numbers of heterotrophic bacteria rose with increasing glucose concentrations. Critical C/N ratios, i.e., ratios between glucose and ammonium in the reservoirs at which no nitrate was found in the culture vessels, of 12.5 and 10.5 were determined at dilution rates of 0.004 and 0.01 h, respectively. Below these critical values, coexistence of the competing species was found. The numbers of nitrifying bacteria decreased more in the presence of flagellates than in their absence, presumably by selective predation on the nitrifying bacteria, either in the liquid culture or on the glass wall of the culture vessels. Despite this, the rate of nitrate production did not decrease more in the presence of flagellates than in their absence. This demonstrates that no correlation has to be expected between numbers of nitrifying bacteria and their activity and that a constant nitrification rate per cell cannot be assumed for nitrifying bacteria. Above the critical C/N ratios, low numbers of nitrifying bacteria were still found in the culture vessels, probably because of attachment of the nitrifying bacteria to the glass wall of the culture vessels. Like the numbers of heterotrophic bacteria, the numbers of flagellates increased when the glucose concentrations in the reservoirs increased. Numbers of 2 x 10 and 12 x 10 flagellates ml were found at 7 mM glucose at dilution rates of 0.004 and 0.01 h, respectively. It was concluded that the critical C/N ratios were practically unaffected by the presence of protozoa. Although nitrate production rates were equal in the presence and absence of flagellates, the numbers of nitrifying bacteria decreased more strongly in their presence. This indicates a higher activity per nitrifying cell in the presence of flagellates.

A validated miniaturized MPN method, based on ISO 6579:2002, for the enumeration of Salmonella from poultry matrices

AIMS

To validate the effectiveness of a miniaturized most probable number method (mMPN) in enumerating Salmonella from poultry matrices.

METHODS AND RESULTS

A MPN was developed, based on the ISO 6579:2002 method using modified semi-solid Rappaport-Vassiliadis media as the sole selective medium. The validation of the mMPN was shown to not differ significantly from, at the 95% confidence level (Student's t-test P = 0·357) to, the traditional 9-tube MPN (tMPN) using pure cultures of Salmonella ser. Typhimurium, Infantis, Montevideo, Muenster and Salmonella subsp II 1,4,12,27:b:[e,n,x] (Sofia). The validation of naturally and artificially contaminated poultry matrices (carcasses, scald tank water, faeces, caeca and feed) showed that detection using the mMPN compared well to the ISO 6572:2002; sensitivity (92%), specificity (97%) and agreement (KAPPA 0·72). The quantitative comparison between the tMPN and mMPN methods showed that 92% of enumerations were less than ± 1 log different (Student's t-test = 0·13). Financial analysis showed that the mMPN required 64% less media and 56% less labour than the tMPN.

CONCLUSION

The mMPN is a consistent, easy to automate method for the enumeration of Salmonella from different poultry matrices.

SIGNIFICANCE AND IMPACT OF STUDY

The miniaturized MPN reduces the material and labour cost of the method and enables the uniform and accurate measurement of the effectiveness of intervention strategies in the control of Salmonella colonization of poultry.

Phylogenetic diversity and axial distribution of microbes in the intestinal tract of the polychaete Neanthes glandicincta

The phylogenetic diversity and axial distribution of microorganisms in three sections of the gastrointestinal tracts of the polychaete Neanthes glandicincta was evaluated using both most probable number method and cloning analyses of 16S rRNA genes in this study. Quantification of the density of microorganisms in the gut showed that aerobic microorganisms decreased from anterior to posterior, while anaerobic ones showed a reverse trend. The total numbers of microorganisms decreased significantly (p < 0.05, analysis of variance) but more rapidly from the anterior to the middle segment. Phylogenetic analysis showed that the dominating phylogenetic groups included Methanomicrobiales I: Methanosaetaceae (up to 66% of archaeal clones), delta-Proteobacteria (up to 42% of bacterial clones), and gamma-Proteobacteria (up to 30% of bacterial clones) widely distributed throughout the entire gut. Other microbiota distributed in different gut sections were Methanomicrobiales II: Methanospirillaceae, Methanomicrobiales III, Thermoplasmatales, Crenarchaea, Methanobacteriaceae, and Methanosarcinales for archaea; and alpha-Proteobacteria, beta-Proteobacteria, Fusobacteria, Clostridia, Chloroflexi, and Planctomycetes for bacteria. The results reveal a difference in microbial community structure along the gut of N. glandicincta. The various phylogenetic diversity and axial distribution of microbes along the gut might indicate an environmental gradient from anterior to posterior sections affecting the structure of the microbial community.

Inhibition of perchlorate reduction by nitrate in a fixed biofilm reactor

Perchlorate and nitrate were reduced simultaneously in fixed biofilm reactors. Reduction of 1000 microg L(-1) perchlorate decreased slightly with the addition of 10-16 mg L(-1) NO(3)-N when excess acetate was supplied while denitrification was complete. When influent acetate was reduced by 50% to well below the stoichiometric requirement, perchlorate reduction decreased by 70% while denitrification decreased by only 20%, suggesting that competition for electrons by nitrate was a factor in inhibition. Reduction of nitrate was favored over perchlorate, even though reactor biofilm had been enriched under perchlorate-reducing conditions for 10 months. When excess acetate was restored, perchlorate and nitrate returned to initial levels. The average most probable numbers of perchlorate- and nitrate-reducing bacteria during excess substrate operation were not significantly different and ranged between 2.0 x 10(5) and 7.9 x 10(5)cells cm(-2) media surface area. The effect of nitrate on chloride generation by suspensions of perchlorate-reducing populations was studied using a chloride ion probe. The rate of reduction of 2mM perchlorate decreased by 30% in the presence of 2mM nitrate when excess acetate was added. When acetate was limited, perchlorate reduction decreased by 70% in the presence of equi-molar nitrate.

Numeration methods for targeting photoactive materials in the UV-A photocatalytic removal of microorganisms

This tutorial review reports on the different numeration methods for evaluating the efficiency of the photocatalytic action on microorganisms. Here we put forward the advantages and drawbacks of the standard methods such as the plate count, the fluorescence techniques and the Most Probable Number method for determining the biocidal photocatalytic activity and thus selecting efficient photocatalytic materials among complex systems. We highlight that bacterial spores are a representative and suitable tool for meeting the restrictive requirements resulting from the complex use of living matter instead of chemical targets.

The effect of soil type and plant age on the population size of rhizospheric methanotrophs and their activities in tropical rice soils

A laboratory incubation experiment was conducted in tropical rain-fed (red soil) and irrigated (black soil) rice agroecosystem during the crop growing season to determine the effect of the type of soil, cultivation practices and the age of plant on MOB (methane oxidizing bacteria) population size and their activities. The average value of MOB population size was 11.7 +/- 4.5 x 10(5) cells g(-1) soil, with a range of 3.1 +/- 0.4 to 21.2 +/- 1.0 x 10(5) cells g(-1) soil for red soil, which was lower in comparison to black soil where population size varied between 84.2 +/- 3.8 and 289.4 +/- 7.0 x 10(5) cells g(-1) soil with an average of 182.8 +/- 53.5 x 10(5) cells g(-1) soil. The highest population size was recorded during the grain maturation stage which gradually declined during the grain filling, flowering and tillering stages of the rice plants. The HSD test indicated a significant variation in the MOB population size with the varying ages of the plant. CH4 oxidizing capacity was higher in black soil as compared to red soil. The highest CH4 oxidizing capacity was found at the grain-filling stage in both the soil types. The differences in soil types and cultivation practices, pattern of variation in MOB population size and methane oxidation were found similar in both the sites under the influence of plant age, even though the detected values differed significantly.

Export of nitrogenous compounds due to incomplete cycling within biological soil crusts of arid lands

Second only to water among limiting factors, nitrogen controls the fertility of most arid regions. Where dry and wet depositions are weak, as in the western US deserts, N inputs rely heavily on biological N(2) fixation. Topsoil cyanobacterial communities known as biological soil crusts (BSCs) are major N(2) fixation hot spots in arid lands, but the fate of their fixed N remains controversial. Using a combination of microscale and mesoscale process rate determinations, we found that, in spite of theoretically optimal conditions, denitrification rates in BSCs were paradoxically immaterial for nitrogen cycling. Denitrifier populations within BSCs were extremely low. Because of this absence of denitrification, and because of the limitation of respiration and ammonia oxidation by diffusive O(2) supply, we could demonstrate that BSCs function as net exporters of ammonium, nitrate and organic N to the soils they cover, in approximately stoichiometrically equal proportions. Overall export rates during periods of biological activity are in the range of tens to hundreds of mumol-N m(-2) h(-1), commensurate with those of N(2) fixation. These results explain the long-term dependence of BSCs on N(2) fixation, confirm their role in landscape fertility, and provide a robust argument for conservation of these endangered communities.

Effluent recirculation to improve perchlorate reduction in a fixed biofilm reactor

The effect of effluent recirculation on perchlorate reduction in a nominally plug-flow fixed biofilm reactor was studied in two cases: influent concentrations of 10 and 400 microg/L at low hydraulic loading rates (1.9 and 37.5 m(3)/m(2)/day without and with recirculation, respectively) and after a step increase in perchlorate concentration to 1,000 microg/L at the higher hydraulic loading rate (5 and 100 m(3)/m(2)/day without and with recirculation, respectively). Complete perchlorate reduction was sustained for influent concentrations of 400 and 10 microg/L in both flow regimes at the lower hydraulic loading rates. Reactor tracer profiles showed that biofilm diffusion had a more significant effect on mass transfer in the plug flow reactor compared with recirculation. The recirculation bioreactor acclimated more rapidly to increased hydraulic and perchlorate mass loading rates with significantly lower effluent perchlorate compared to the plug flow reactor: 16 microg/L versus 46 microg/L, respectively, although complete perchlorate removal was not achieved in either flow regime after 21 days acclimation to the higher loading. Total biofilm mass was more uniformly distributed in the recirculation reactor which may have contributed to better performance under increased perchlorate loading.

Removal of H(2)S by Thiobacillus denitrificans immobilized on different matrices

Biological removal of high concentrations of H(2)S was studied using the immobilized Thiobacillus denitrificans with peat moss, wood chip, ceramic and granular activated carbon (GAC) separately. Experiments on the physical adsorption capacity of matrix, retention time and pressure drop were carried out; the ability of bioreactor to buffer shock loading and the removal efficiency with different packing materials were also investigated. Besides, the kinetics of single-stage biodesulfuration was analyzed. The results showed that GAC provided higher bacteria adsorption capacity, showed a more resistance to shock loading and allowed better operational control with respect to pressure drop than other inert carriers. When the retention time was changed from 30 to 100 s at an influent concentration of 100 mg/L of H(2)S, the removal efficiencies were above 98%; when the inlet concentration of H(2)S were changed from 110 to 120 mg/L, an average 96.8% removal efficiency was achieved during the long-term operation for GAC bioreactor. Next to GAC, wood chip was found to be a good packing material; however, peat moss and ceramic had limited effectiveness and their removal efficiencies were less of 90%. The kinetic analysis showed that the maximum removal rate and the half-saturation constant of the GAC bioreactor were 666.7 mg (H(2)S)/(L.d) and 20.8 mg/L, respectively.

Animal–plant–microbe interactions: direct and indirect effects of swan foraging behaviour modulate methane cycling in temperate shallow wetlands

Wetlands are among the most important ecosystems on Earth both in terms of productivity and biodiversity, but also as a source of the greenhouse gas CH(4). Microbial processes catalyzing nutrient recycling and CH(4) production are controlled by sediment physico-chemistry, which is in turn affected by plant activity and the foraging behaviour of herbivores. We performed field and laboratory experiments to evaluate the direct effect of herbivores on soil microbial activity and their indirect effects as the consequence of reduced macrophyte density, using migratory Bewick's swans (Cygnus columbianus bewickii Yarrell) feeding on fennel pondweed (Potamogeton pectinatus L.) tubers as a model system. A controlled foraging experiment using field enclosures indicated that swan bioturbation decreases CH(4) production, through a decrease in the activity of methanogenic Archaea and an increased rate of CH(4) oxidation in the bioturbated sediment. We also found a positive correlation between tuber density (a surrogate of plant density during the previous growth season) and CH(4) production activity. A laboratory experiment showed that sediment sterilization enhances pondweed growth, probably due to elimination of the negative effects of microbial activity on plant growth. In summary, the bioturbation caused by swan grazing modulates CH(4) cycling by means of both direct and indirect (i.e. plant-mediated) effects with potential consequences for CH(4) emission from wetland systems.

Application of cation-exchange membranes for characterisation and imaging ammonia-oxidising bacteria in soils

A new approach, in which ammonia-oxidizing bacteria (AOB) are entrapped from soil onto cation-exchange membranes, was applied to identify terrestrial AOB by fluorescence in situ hybridization (FISH). An experimental hot spot of ammonia oxidation was developed by establishing a gradient of ammonium substrate (200 to <20 mg NH4+-N l(-1)) diffused through the cation-exchange membranes incubated in soil for 6 months. By this approach we were able to characterise and image indigenous AOB populations growing in heavily oil-polluted soil using FISH and sequence analysis of PCR-amplified 16S rRNA genes, respectively. The FISH results revealed that Nitrosospira-like AOB were dominant on the ammonium-enriched membranes incubated in the soil. Fourteen unique Nitrosospira-like 16S rRNA gene sequences belonging to clusters 2 and 3 were recovered from the soil-incubated membranes and from the soil, suggesting the importance of Nitrosospira-like AOB in the oil-polluted landfarming soil.

Nitrogen turnover in drying sediments of an Amazon floodplain lake

In the Amazon floodplain large areas are subject to annual cycles of drying and rewetting. The turnover of nitrogen in the periodically drying sediments is an important regulator of floodplain fertility. In the present study the transition of a lake sediment from flooded to dry conditions was studied with respect to microbial nitrogen turnover. Soil nitrogen pools, as well as the activity and abundance of denitrifying and nitrifying bacteria, were investigated during one dry season. During the first weeks after drying, most of the inorganic nitrogen vanished from the sediment. The process was inhibited by a nitrification inhibitor, showing that coupled nitrification-denitrification was responsible for the nitrogen loss. Assimilation by plants or microbes, as well as leaching, were not important mechanisms of nitrogen loss. During a period of only 10 days, 59% of the total denitrification and 94% of the total N2O emission during the dry period occurred. Cell numbers of denitrifiers were not correlated with activities. Denitrification was not correlated with other sediment variables but was regulated by the patchy distribution of reduced and oxidized zones in the uppermost centimeters of the sediment. This heterogeneity was probably introduced by the bioturbation of small insects, which was restricted to a rather short time period shortly after drying.

Comparing field and microcosm experiments: a case study on methano- and methylo-trophic bacteria in paddy soil

Methane-oxidising bacteria (MOB) play an important role in the reduction of methane emissions from rice agriculture. In rice fields, they are subjected to many environmental and field management parameters, which may have a significant impact on their community composition. To study this in greater detail, the community structure of methano- and methylo-trophic bacteria was investigated in a rice field in northern Italy during the summer 1999 and compared to a microcosm study described previously. We used PCR-based denaturing gradient gel electrophoresis applying 16S rDNA (9alpha and 10gamma) and mxaF (methanol-dehydrogenase) primer sets. In parallel, population size and activity of MOB were determined. This study provides the first comprehensive investigation of different compartments (bulk soil, rhizosphere, rhizoplane, and homogenate) throughout an entire rice-growing season in the field. Lower cell numbers of MOB were detected in the field compared to the microcosms, possibly due to lower CH4 concentrations in the soil pore water. In both studies, growth of MOB occurred predominantly at the root surface (rhizoplane) and in the root (homogenate), whereas cell numbers in bulk soil showed only minor changes throughout the season. Molecular analysis detected only few changes in alpha-proteobacterial methylotrophs during the season, whereas a higher variability was detected in gamma-proteobacteria. Nevertheless, the sequences of electrophoretic bands showed that the diversity in the field study and in the microcosms was comparable. Activity patterns of MOB and the population structure of methylotrophic bacteria agreed well between both studies, even though the detected quantities differed. Extrapolations of microcosm data to the field scale are thus possible, but should be used carefully when concerning quantitative changes.

Relevance of ammonium oxidation within biological soil crust communities

Thin, vertically structured topsoil communities that become ecologically important in arid regions (biological soil crusts or BSCs) are responsible for much of the nitrogen inputs into pristine arid lands. We studied N(2) fixation and ammonium oxidation (AO) at subcentimetre resolution within BSCs from the Colorado Plateau. Pools of dissolved porewater nitrate/nitrite, ammonium and organic nitrogen in wetted BSCs were high in comparison with those typical of aridosoils. They remained stable during incubations, indicating that input and output processes were of similar magnitude. Areal N(2) fixation rates (6.5-48 micromol C(2)H(2) m(-2) h(-1)) were high, the vertical distribution of N(2) fixation peaking close to the surface if populations of heterocystous cyanobacteria were present, but in the subsurface if they were absent. Areal AO rates (19-46 micromol N m(-2) h(-1)) were commensurate with N(2) fixation inputs. When considering oxygen availability, AO activity invariably peaked 2-3 mm deep and was limited by oxygen (not ammonium) supply. Most probable number (MPN)-enumerated ammonia-oxidizing bacteria (6.7-7.9 x 10(3) cells g(-1) on average) clearly peaked at 2-3 mm depth. Thus, AO (hence nitrification) is a spatially restricted but important process in the nitrogen cycling of BSC, turning much of the biologically fixed nitrogen into oxidized forms, the fate of which remains to be determined.

New DGGE strategies for the analyses of methanotrophic microbial communities using different combinations of existing 16S rRNA-based primers

Methane-oxidising microbial communities are studied intensively because of their importance for global methane cycling. A suite of molecular microbial techniques has been applied to the study of these communities. Denaturing gradient gel electrophoresis (DGGE) is a diversity screening tool combining high sample throughput with phylogenetic information of high resolution. The existing 16S rRNA-based DGGE assays available for methane-oxidising bacteria suffer from low-specificity, low phylogentic information due to the length of the amplified fragments and/or from lack of resolving power. In the present study we developed new combinations of existing primers and applied these on methane-oxidising microbial communities in a freshwater wetland marsh. The designed strategies comprised nested as well as direct amplification of environmental DNA. Successful application of direct amplification using combinations of universal and specific primers circumvents the nested designs currently used. All developed assays resulted in identical community profiles in wetland soil cores with Methylobacter sp. and Methylocystis sp.-related sequences. Changes in the occurrence of Methylobacter-related sequences with depth in the soil profile may be related to the decrease in methane-oxidizing activity.

Occurrence of nitrifiers and diversity of ammonia-oxidizing bacteria in developing drinking water biofilms

We studied the population dynamics of nitrifying bacteria during the development of biofilms up to 233 or 280 days on polyvinylchloride pipes connected to two full-scale drinking water distribution networks supplying processed and chloraminated surface water. The numbers of nitrifiers in biofilms were enumerated at intervals of 10-64 days by the most probable number (MPN) method at waterworks and at several study sites in distribution network areas. The numbers of nitrifiers increased towards the distal sites. The highest detected MPN counts of ammonia-oxidizing bacteria (AOB) for study areas 1 and 7 were 500 MPN cm(-2) and 1.0 x 10(6) MPN cm(-2), and those of nitrite-oxidizing bacteria (NOB) 96 MPN cm(-2) and 2.2 x 10(3) MPN cm(-2), respectively. The diversity of AOB was determined by PCR amplifying, cloning and sequencing the partial ammonia monooxygenase (amoA) gene of selected biofilm samples presenting different biofilm ages. The PCR primers used, A189 and A682, also amplified a fragment of particulate methane monooxygenase (pmoA) gene of methane-oxidizing bacteria. The majority of biofilm clones (24 out of 30 studied) contained Nitrosomonas amoA-like sequences. There were only two pmoA-like sequences of Type I methanotrophs, and four sequences positioned in amoA/pmoA sequence groups of uncultured bacteria. From both study area very similar or even completely identical Nitrosomonas amoA-like sequences were obtained despite of high difference in AOB numbers. The results show that the conditions in newly formed biofilms in drinking water distribution systems favor the growth of Nitrosomonas-type AOB.

Long-term behavior of passively aerated compost methanotrophic biofilter columns

The methane oxidation potential of several types of compost methanotrophic biofilter columns were compared in the laboratory over a period of 220 days. The results indicate an increase in methanotrophic activity over a period of about 100 days, up to a maximum of 400 g m(-2) day(-1), and a gradual decline to about 100 g m(-2) day(-1) within the next 120 days. High methane oxidation rates appear to be restricted to a small area of the column, 10-15 cm thick. Based on the laboratory investigations carried out to determine the cause for the decline in methane oxidation rate, it was concluded that the formation of exopolymeric substances (EPS), at the zones of maximum methane oxidation, was responsible for this decline. In monitoring methane oxidation in a column for up to 600 days, it was observed that mixing of the medium after formation of EPS enabled the column to temporarily recover high performance. The results suggest that stable, homogenous compost, with a low C/N and low ammonium content, mixed on a regular basis, could achieve and maintain high methane oxidation efficiencies.

Alcanivorax which prevails in oil-contaminated seawater exhibits broad substrate specificity for alkane degradation

Alcanivorax is an alkane-degrading marine bacterium which propagates and becomes predominant in crude-oil-containing seawater when nitrogen and phosphorus nutrients are supplemented. In order to understand why Alcanivorax overcomes other bacteria under such cultural conditions, competition experiments between Alcanivorax indigenous to seawater and the exogenous alkane-degrading marine bacterium, Acinetobacter venetianus strain T4, were conducted. When oil-containing seawater supplemented with nitrogen and phosphorus nutrients was inoculated with A. venetianus strain T4, this bacterium was the dominant population at the early stage of culture. However, its density began to decrease after day 6, and Alcanivorax predominated in the culture after day 20. The crude-oil-degrading profiles of both bacteria were therefore investigated. Alcanivorax borkumensis strain ST-T1 isolated from the Sea of Japan exhibited higher ability to degrade branched alkanes (pristane and phytane) than A. venetianus strain T4. It seems that this higher ability of Alcanivorax to degrade branched alkanes allowed this bacterium to predominate in oil-containing seawater. It is known that some marine zooplanktons produce pristane and Alcanivorax may play a major role in the biodegradation of pristane in seawater.

Immunogenicity and protective effects of truncated recombinant leukotoxin proteins of Fusobacterium necrophorum in mice

Fusobacterium necrophorum, a gram-negative, anaerobic and rod-shaped bacterium, is generally an opportunistic pathogen and causes a wide variety of necrotic infections in animals and humans. Leukotoxin, a secreted protein, is a major virulence factor. The gene encoding the leukotoxin (lktA) in F. necrophorum has been cloned, sequenced and expressed in Escherichia coli. Because of low expression levels, problems associated with purifying full-length recombinant protein, and of the physical instability of the protein, five overlapping leukotoxin gene truncations were constructed. The recombinant polypeptides (BSBSE, SX, GAS, SH, and FINAL) were expressed in E. coli and purified by nickel-affinity chromatography. The objectives were to investigate the effectiveness of the purified truncated polypeptides to induce protective immunity in mice challenged with F. necrophorum. The polypeptides, individually or in combination, and inactivated native leukotoxin or culture supernatant of F. necrophorum were homogenized with an adjuvant and injected into mice on days 0 and 21. Blood samples were collected to measure serum anti-leukotoxin antibody titers on days 0, 21 and 42 and on day 42, mice were experimentally challenged with F. necrophorum. All polypeptides were immunogenic, with GAS polypeptide eliciting the least antibody response. Two polypeptides (BSBSE and SH) induced significant protection in mice against F. necrophorum infection. Protection was better than the full-length native leukotoxin or inactivated supernatant.The study demonstrated that the leukotoxin of F. necrophorum carries epitopes that induce protective immunity against experimental fusobacterial infection, thus providing further evidence to the importance of leukotoxin as a major virulence factor.