Microtechnique for most-probable-number analysis

Influence of heterotrophic microbial growth on biological oxidation of pyrite

The rate and extent of pyrite oxidation by the iron-oxidizing bacteria Acidithiobacillus ferrooxidans was limited by the growth of the heterotrophic microbe Acidiphilium acidophilum. In batch systems containing a mixture of both organisms, the maximum zero-order rate of ferric iron accumulation was about 1.4 mg of Fe3+ L(-1) d(-1) as compared to 9.4 mg of Fe3+ L(-1) d(-1) for pure cultures of A. ferrooxidans under the same conditions. Pyrite oxidation was limited in cases where both cultures of organisms were initially present as well as situations where the heterotrophic organisms were added to established, pyrite-oxidizing systems containing A. ferrooxidans. Results also indicated that organic carbon remaining in solution following heterotrophic bacterial growth reduced the rate of abiotic pyrite oxidation by the ferric ion. Furthermore, a cell-free solution of the residual organic carbon resulted in a lag of A. ferrooxidans growth in soluble ferrous medium. The residual organic carbon solution that accumulated during the growth of Aph. acidophilum had a diverse molecular weight distribution, indicating that different compounds could be responsible for the inhibition of chemical pyrite oxidation and the A. ferrooxidans growth lag observed. Titration of dissolved copper ions with residual dissolved organic carbon originating from Aph. acidophilum cultures indicated that a metal complexation mechanism could be responsible for the lower rates of pyrite oxidation observed. These data suggest that encouraging the growth of heterotrophic microorganisms under acid mine drainage conditions may be a feasible strategy for decreasing both the rate and the extent of sulfide mineral oxidation.

Occurrence of nitrifying bacteria and nitrification in Finnish drinking water distribution systems

Microbiological nitrification process may lead to chemical, microbiological and technical problems in drinking water distribution systems. Nitrification activity is regulated by several physical, and chemical, and operational factors. However, the factors affecting nitrification in the distribution systems in boreal region, having its specific environmental characteristics, are poorly known. We studied the occurrence and activity of nitrifying bacteria in 15 drinking water networks distributing water with very different origin and treatment practices. The waters included chloraminated surface water, chlorinated surface water, and non-disinfected groundwater. The networks were located in eight towns in different parts of Finland. Our results showed that nitrifying bacteria are common in boreal drinking water distribution systems despite their low temperature. Surprisingly high numbers and activities of nitrifiers were detected in pipeline sediment samples. The numbers of ammonia-oxidizing bacteria and their oxidation potentials were highest in chloraminated drinking water delivering networks, whereas the nitrite-oxidizing bacteria were present in the greatest numbers in those networks that used non-disinfected groundwater. The occurrence of nitrifying bacteria in drinking water samples correlated positively with the numbers of heterotrophic bacteria and turbidity, and negatively with the content of total chlorine. Although nitrifying bacteria grew well in drinking water distribution systems, the problems with nitrite accumulation are rare in Finland.

Changes in activity and community structure of methane-oxidizing bacteria over the growth period of rice

The activity and community structure of methanotrophs in compartmented microcosms were investigated over the growth period of rice plants. In situ methane oxidation was important only during the vegetative growth phase of the plants and later became negligible. The in situ activity was not directly correlated with methanotrophic cell counts, which increased even after the decrease in in situ activity, possibly due to the presence of both vegetative cells and resting stages. By dividing the microcosms into two soil and two root compartments it was possible to locate methanotrophic growth and activity, which was greatest in the rhizoplane of the rice plants. Molecular analysis by denaturing gradient gel electrophoresis and fluorescent in situ hybridization (FISH) with family-specific probes revealed the presence of both families of methanotrophs in soil and root compartments over the whole season. Changes in community structure were detected only for members of the Methylococcaceae and could be associated only with changes in the genus Methylobacter and not with changes in the dominance of different genera in the family Methylococcaceae. For the family Methylocystaceae stable communities in all compartments for the whole season were observed. FISH analysis revealed evidence of in situ dominance of the Methylocystaceae in all compartments. The numbers of Methylococcaceae cells were relatively high only in the rhizoplane, demonstrating the importance of rice roots for growth and maintenance of methanotrophic diversity in the soil.

Effects of agronomic treatments on structure and function of ammonia-oxidizing communities

The aim of this study was to determine the effects of different agricultural treatments and plant communities on the diversity of ammonia oxidizer populations in soil. Denaturing gradient gel electrophoresis (DGGE), coupled with specific oligonucleotide probing, was used to analyze 16S rRNA genes of ammonia oxidizers belonging to the beta subgroup of the division Proteobacteria by use of DNA extracted from cultivated, successional, and native deciduous forest soils. Community profiles of the different soil types were compared with nitrification rates and most-probable-number (MPN) counts. Despite significant variation in measured nitrification rates among communities, there were no differences in the DGGE banding profiles of DNAs extracted from these soils. DGGE profiles of DNA extracted from samples of MPN incubations, cultivated at a range of ammonia concentrations, showed the presence of bands not amplified from directly extracted DNA. Nitrosomonas-like bands were seen in the MPN DNA but were not detected in the DNA extracted directly from soils. These bands were detected in some samples taken from MPN incubations carried out with medium containing 1,000 microg of NH(4)(+)-N ml(-1), to the exclusion of bands detected in the native DNA. Cell concentrations of ammonia oxidizers determined by MPN counts were between 10- and 100-fold lower than those determined by competitive PCR (cPCR). Although no differences were seen in ammonia oxidizer MPN counts from the different soil treatments, cPCR revealed higher numbers in fertilized soils. The use of a combination of traditional and molecular methods to investigate the activities and compositions of ammonia oxidizers in soil demonstrates differences in fine-scale compositions among treatments that may be associated with changes in population size and function.

Quantitative analysis of ammonia oxidising bacteria using competitive PCR

Culture-based methods for enumeration, such as most probable number (MPN) methodologies, have proved inefficient due to difficulties in the isolation and cultivation of ammonia oxidising bacteria in the laboratory. Biases are associated with the isolation of bacteria in selective media and organisms cultivated in the laboratory may not be truly representative of those in the environment. In this study, we developed a competitive PCR (cPCR)-based method based on the amplification of 16S rRNA genes specific for the beta-subgroup proteobacterial ammonia oxidising bacteria for enumeration of these organisms. Populations in both agricultural soils and estuarine sediments were quantified by traditional MPN and by cPCR. The numbers of ammonia oxidisers for both sample types were significantly underestimated by conventional MPN and were 1-3 orders of magnitude lower than those obtained by cPCR. Higher numbers of ammonia oxidisers found in fertilised plots in agricultural soils by the cPCR technique were not observed in MPN estimates. It was necessary to construct a separate standard curve for each sample type as differences in DNA extraction, quantity and purity had a significant bearing on the ease of PCR of both competitor and target DNA.

Comparison of organic and inorganic packing materials in the removal of ammonia gas in biofilters

Two organic and two inorganic packing materials were compared with regard to the removal of ammonia gas in a biofilter inoculated with night-soil sludge. By gradually increasing the inlet load of ammonia, the complete removal capacity, which was defined as the inlet load of ammonia that was completely removed, and the maximum removal capacity of ammonia, which was the value when the removal capacity leveled off for each packing material, were estimated. Both values which were based on a unit volume of packing material, were higher for organic packing materials than inorganic ones. By using kinetic analysis, the maximum removal rate of ammonia, V(m), and the saturation constant, K(s), were determined for all packing materials and the values of V(m) for organic packing materials were found to be larger. By using the kinetic parameters, the removal rates for ammonia were compared among the four packing materials, and the organic packing materials showed superior performance for the removal of ammonia in the concentration range of 0-300 ppm as compared to inorganic packing materials.

Stimulating accumulation of nitrifying bacteria in porous carrier by addition of inorganic carbon in a continuous-flow fluidized bed wastewater treatment reactor

Porous polyurethane carrier particles have been successfully applied for microbial immobilization to simultaneously remove carbonaceous and nitrogenous substances from wastewater by a fill-and-draw operation. This reactor system was extended to a continuous-flow operation mode, by which inorganic carbon (IC) was supplemented in order to stimulate the growth of autotrophic nitrifying bacteria. By addition of sodium bicarbonate, the ammonia oxidation reaction proceeded remarkably in the porous particle fluidized bed reactor, while a small increase in the nitrification was observed in a reactor with suspended microbes. Dissolved oxygen profile was obtained using an oxygen microelectrode to measure the microbial consumption of oxygen in the porous carrier. The size of ammonia-oxidizing bacterial populations in the carrier was proportional to the volume of the aerobic region of the carrier. The aerobic region decreased with the increase in sodium bicarbonate concentration, which improved the ammonia-oxidizing activity of retained nitrifiers in the carrier. The maximum ammonia oxidation rate was up to 55.6 gN/m3/h within the aerobic region of the carrier under the following feed conditions: 100 mg/l of total organic compound, 55 mg/l of ammonium concentration and 48 mg/l of inorganic carbon.

Nitrification and autotrophic nitrifying bacteria in a hydrocarbon-polluted soil

In vitro ammonia-oxidizing bacteria are capable of oxidizing hydrocarbons incompletely. This transformation is accompanied by competitive inhibition of ammonia monooxygenase, the first key enzyme in nitrification. The effect of hydrocarbon pollution on soil nitrification was examined in situ. In a microcosm study, adding diesel fuel hydrocarbon to an uncontaminated soil (agricultural unfertilized soil) treated with ammonium sulfate dramatically reduced the amount of KCl-extractable nitrate but stimulated ammonium consumption. In a soil with long history of pollution that was treated with ammonium sulfate, 90% of the ammonium was transformed into nitrate after 3 weeks of incubation. Nitrate production was twofold higher in the contaminated soil than in the agricultural soil to which hydrocarbon was not added. To assess if ammonia-oxidizing bacteria acquired resistance to inhibition by hydrocarbon, the contaminated soil was reexposed to diesel fuel. Ammonium consumption was not affected, but nitrate production was 30% lower than nitrate production in the absence of hydrocarbon. The apparent reduction in nitrification resulted from immobilization of ammonium by hydrocarbon-stimulated microbial activity. These results indicated that the hydrocarbon inhibited nitrification in the noncontaminated soil (agricultural soil) and that ammonia-oxidizing bacteria in the polluted soil acquired resistance to inhibition by the hydrocarbon, possibly by increasing the affinity of nitrifying bacteria for ammonium in the soil.

Comparative diversity of ammonia oxidizer 16S rRNA gene sequences in native, tilled, and successional soils

Autotrophic ammonia oxidizer (AAO) populations in soils from native, tilled, and successional treatments at the Kellogg Biological Station Long-Term Ecological Research site in southwestern Michigan were compared to assess effects of disturbance on these bacteria. N fertilization effects on AAO populations were also evaluated with soils from fertilized microplots within the successional treatments. Population structures were characterized by PCR amplification of microbial community DNA with group-specific 16S rRNA gene (rDNA) primers, cloning of PCR products and clone hybridizations with group-specific probes, phylogenetic analysis of partial 16S rDNA sequences, and denaturing gradient gel electrophoresis (DGGE) analysis. Population sizes were estimated by using most-probable-number (MPN) media containing varied concentrations of ammonium sulfate. Tilled soils contained higher numbers than did native soils of culturable AAOs that were less sensitive to different ammonium concentrations in MPN media. Compared to sequences from native soils, partial 16S rDNA sequences from tilled soils were less diverse and grouped exclusively within Nitrosospira cluster 3. Native soils yielded sequences representing three different AAO clusters. Probes for Nitrosospira cluster 3 hybridized with DGGE blots from tilled and fertilized successional soils but not with blots from native or unfertilized successional soils. Hybridization results thus suggested a positive association between the Nitrosospira cluster 3 subgroup and soils amended with inorganic N. DGGE patterns for soils sampled from replicated plots of each treatment were nearly identical for tilled and native soils in both sampling years, indicating spatial and temporal reproducibility based on treatment.

Nitrogen cycling and community structure of proteobacterial beta-subgroup ammonia-oxidizing bacteria within polluted marine fish farm sediments

A multidisciplinary approach was used to study the effects of pollution from a marine fish farm on nitrification rates and on the community structure of ammonia-oxidizing bacteria in the underlying sediment. Organic content, ammonium concentrations, nitrification rates, and ammonia oxidizer most-probable-number counts were determined in samples of sediment collected from beneath a fish cage and on a transect at 20 and 40 m from the cage. The data suggest that nitrogen cycling was significantly disrupted directly beneath the fish cage, with inhibition of nitrification and denitrification. Although visual examination indicated some slight changes in sediment appearance at 20 m, all other measurements were similar to those obtained at 40 m, where the sediment was considered pristine. The community structures of proteobacterial beta-subgroup ammonia-oxidizing bacteria at the sampling sites were compared by PCR amplification of 16S ribosomal DNA (rDNA), using primers which target this group. PCR products were analyzed by denaturing gradient gel electrophoresis (DGGE) and with oligonucleotide hybridization probes specific for different ammonia oxidizers. A DGGE doublet observed in PCR products from the highly polluted fish cage sediment sample was present at a lower intensity in the 20-m sample but was absent from the pristine 40-m sample station. Band migration, hybridization, and sequencing demonstrated that the doublet corresponded to a marine Nitrosomonas group which was originally observed in 16S rDNA clone libraries prepared from the same sediment samples but with different PCR primers. Our data suggest that this novel Nitrosomonas subgroup was selected for within polluted fish farm sediments and that the relative abundance of this group was influenced by the extent of pollution.

Application of molecular biological techniques to a seasonal study of ammonia oxidation in a eutrophic freshwater lake

The autotrophic ammonia-oxidizing bacteria in a eutrophic freshwater lake were studied over a 12-month period. Numbers of ammonia oxidisers in the lakewater were small throughout the year, and tangential-flow concentration was required to obtain meaningful estimates of most probable numbers. Sediments from littoral and profundal sites supported comparatively large populations of these bacteria, and the nitrification potential was high, particularly in summer samples from the littoral sediment surface. In enrichment cultures, lakewater samples nitrified at low (0.67 mM) ammonium concentrations only whereas sediment samples exhibited nitrification at high (12.5 mM) ammonium concentrations also. Enrichments at low ammonium concentration did not nitrify when inoculated into high-ammonium medium, but the converse was not true. This suggests that the water column contains a population of ammonia oxidizers that is sensitive to high ammonium concentrations. The observation of nitrification at high ammonium concentration by isolates from some winter lakewater samples, identified as nitrosospiras by 16S rRNA probing, is consistent with the hypothesis that sediment ammonia oxidizers enter the water column at overturn. With only one exception, nested PCR amplification enabled the detection of Nitrosospira 16S rDNA in all samples, but Nitrosomonas (N. europaea-eutropha lineage) 16S rDNA was never obtained. However, the latter were part of the sediment and water column communities, because their 16S rRNA could be detected by specific oligonucleotide probing of enrichment cultures. Furthermore, a specific PCR amplification regime for the Nitrosomonas europaea ammonia monooxygenase gene (amoA) yielded positive results when applied directly to sediment and lakewater samples. Patterns of Nitrosospira and Nitrosomonas detection by 16S rRNA oligonucleotide probing of sediment enrichment cultures were complex, but lakewater enrichments at low ammonium concentration were positive for nitrosomonads and not nitrosospiras. Analysis of enrichment cultures has therefore provided evidence for the existence of subpopulations within the lake ammonia-oxidizing community distinguishable on the basis of ammonium tolerance and possibly showing a seasonal distribution between the sediment and water column.

Enumeration of acetogens by a colorimetric most-probable-number assay

Anaerobic O demethylation by acetogenic bacteria often is the first step in the mineralization of methoxylated aromatic compounds in anoxic environments. In this reaction, an ether bond is cleaved and the resulting methyl group is metabolized via the acetyl coenzyme A pathway (acetogenesis). Anaerobic O demethylation was used to assess acetogen populations. Environmental samples were diluted in anaerobic medium containing a methoxylated aromatic substrate (vanillate) and titanium(III), and acetogen titers were estimated by the most-probable-number (MPN) method. Complex formation between Ti(III) and vicinal hydroxyl groups of the aromatic products of anaerobic O demethylation results in the development of a yellow color in the medium, which can be detected by eye and monitored spectrophotometrically. High-performance liquid chromatography analysis of the yellow MPN tubes showed that they contained the product of anaerobic O demethylation of vanillate (protocatechuate). This assay was used to enumerate O-demethylating acetogen populations in environmental samples.

Measurement of hydrocarbon-degrading microbial populations by a 96-well plate most-probable-number procedure

A 96-well microtiter plate most-probable-number (MPN) procedure was developed to enumerate hydrocarbon-degrading microorganisms. The performance of this method, which uses number 2 fuel oil (F2) as the selective growth substrate and reduction of iodonitrotetrazolium violet (INT) to detect positive wells, was evaluated by comparison with an established 24-well microtiter plate MPN procedure (the Sheen Screen), which uses weathered North Slope crude oil as the selective substrate and detects positive wells by emulsification or dispersion of the oil. Both procedures gave similar estimates of the hydrocarbon-degrader population densities in several oil-degrading enrichment cultures and sand samples from a variety of coastal sites. Although several oils were effective substrates for the 96-well procedure, the combination of F2 with INT was best, because the color change associated with INT reduction was more easily detected in the small wells than was disruption of the crude oil slick. The method's accuracy was evaluated by comparing hydrocarbon-degrader MPNs with heterotrophic plate counts for several pure and mixed cultures. For some organisms, it seems likely that a single cell cannot initiate sufficient growth to produce a positive result. Thus, this and other hydrocarbon-degrader MPN procedures might underestimate the hydrocarbon-degrading population, even for culturable organisms.

Bioluminescent Most-Probable-Number Method To Enumerate lux -Marked Pseudomonas aeruginosa UG2Lr in Soil

Bioluminescence measured with a luminometer and charge-coupled device was an effective marker in most-probable-number assays for luxAB -marked Pseudomonas aeruginosa UG2Lr in soil. Most-probable-number assays with microtiter plate wells and luminometer tubes gave estimates for UG2Lr that were similar to viable colony counts. Both methods detected five cells per g of soil.

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

The enhanced mineralization of immobilized nitrogen by bacteriophagous protozoa has been thought to favor the nitrification process in soils in which nitrifying bacteria must compete with heterotrophic bacteria for the available ammonium. To obtain more insight into this process, the influence of grazing by the flagellate Adriamonas peritocrescens on the competition for ammonium between the chemolithotrophic species Nitrosomonas europaea and the heterotrophic species Arthrobacter globiformis in the presence of Nitrobacter winogradskyi was studied in soil columns, which were continuously percolated with media containing 5 mM ammonium and different amounts of glucose at a dilution rate of 0.007 h -1 (liquid volumes). A. globiformis won the competition for ammonium. The grazing activities of the flagellates had two prominent effects on the competition between N. europaea and A. globiformis . First, the distribution of ammonium over the profile of the soil columns was more uniform in the presence of flagellates than in their absence. In the absence of flagellates, relatively high amounts of ammonium accumulated in the upper layer (0 to 3 cm), whereas in the underlying layers the ammonium concentrations were low. In the presence of flagellates, however, considerable amounts of ammonium were found in the lower layers, whereas less ammonium accumulated in the upper layer. Second, the potential ammonium-oxidizing activity of N. europaea was stimulated in the presence of flagellates. The numbers of N. europaea at different glucose concentrations in the presence of flagellates were comparable to those in the absence of protozoa. However, in the presence of flagellates, the potential ammonium-oxidizing activities were four to five times greater than those in the absence of protozoa.

Competition for Ammonium between Nitrifying and Heterotrophic Bacteria in Dual Energy-Limited Chemostats

The absence of nitrification in soils rich in organic matter has often been reported. Therefore, competition for limiting amounts of ammonium between the chemolithotrophic 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 −1 . Ammonium limitation of A. globiformis was achieved by increasing the glucose concentration in the reservoir stepwise from 0 to 5 mM while maintaining the ammonium concentration at 2 mM. The numbers of N. europaea and N. winogradskyi cells decreased as the numbers of heterotrophic bacteria rose with increasing glucose concentrations for both dilution rates. Critical carbon-to-nitrogen ratios of 11.6 and 9.6 were determined for the dilution rates of 0.004 and 0.01 h −1 , respectively. Below these critical values, coexistence of the competing species was found in steady-state situations. Although the numbers were strongly reduced, the nitrifying bacteria were not fully outcompeted by the heterotrophic bacteria above the critical carbon-to-nitrogen ratios. Nitrifying bacteria could probably maintain themselves in the system above the critical carbon-to-nitrogen ratios because they are attached to the glass wall of the culture vessels. The numbers of N. europaea decreased more than did those of N. winogradskyi . This was assumed to be due to heterotrophic growth of the latter species on organic substrates excreted by the heterotrophic bacteria.

Quantitative relationship between oral nitrate-reducing activity and the endogenous formation of N-nitrosoamino acids in humans

Salivary nitrate and nitrate concentrations, in vitro kinetics of nitrate reduction in saliva, and numbers of salivary nitrate-reducing micro-organisms were each compared with N-nitrosoamino acid excretion in 16 humans eating controlled diets. N-Nitrosoproline (NPRO) and N-nitrosothiazolidine-4-carboxylic acid (NTCA) excretion were measured after intake of nitrate (5.24 mmol) and L-proline (4.35 mmol) before and after treatment with an oral antiseptic (Peridex, 0.12% chlorhexidine gluconate). Peridex treatment resulted in a 94% reduction in the numbers of salivary nitrate-reducing bacteria, a decline from 17 to 4% in the amount of salivary nitrate that was reduced to nitrite in vivo, and an 85% reduction in the rate of in vitro nitrate reduction by saliva. Concurrently, there were 62 and 74% inhibitions of endogenous NPRO and NTCA formation, respectively. Correlations of the numbers of nitrate reductase micro-organisms, in vivo oral nitrate reduction and salivary nitrite concentrations, with individual NPRO excretion, indicated that individuals with higher oral nitrate-reducing capacities formed more N-nitrosoamino acid endogenously. These data suggest that individual differences in oral nitrate reduction are a significant factor in gastric nitrosation and account for a large proportion of the interindividual variability in nitrosoamino acid excretion.

Dynamics of microbial populations in soil: Indigenous microorganisms degrading 2,4-dinitrophenol

The mineralization of 2,4-dinitrophenol (DNP) and changes in the DNP-mineralizing population over a wide range of DNP concentrations were monitored to evaluate the dynamics of the DNP-mineralizing populations in two soils (soils 1 and 2). Curves of CO2 evolution were analyzed using nonlinear regression analysis and models incorporating parameters for population size and growth rate. The results of these analyses were compared to independent estimates of the DNP-mineralizing population from most-probable-number (MPN) determinations. The combined results of these analyses showed that 0.1μg of DNP g(-1) of soil was too low a concentration to support maintenance or growth of the DNP-mineralizing population, whereas all higher concentrations supported either maintenance or growth of the population in soil 1. Independent estimates of population size showed good agreement between the nonlinear regression and MPN techniques, especially at initial DNP concentrations below 100μg g(-1). Estimates of both population size and maximum specific growth rate varied with concentration, possibly indicating the existence of two different DNP-mineralizing populations in soil 1. In the other soil tested (soil 2), the population of DNP-mineralizers was much lower than in the first soil, and no evidence of two populations was obtained. In soil 2, good agreement between the nonlinear regression and MPN estimates of population size was also obtained. Results of this study demonstrate the power of using testable models of population dynamics to obtain useful estimates of parameters of microbial growth and survival in soil.

Nutritional characteristics of a mixotrophic nanoflagellate,Ochromonas sp

Autotrophic and heterotrophic growth characteristics of a nano-flagellate were investigated. The flagellate,Ochromonas sp., was isolated from the northern Baltic Sea. Autotrophic growth was poor. Axenically pregrown flagellates did not increase significantly in cell number during incubation in different inorganic media. The number of flagellates remained constant 3-5 weeks in cultures kept in the light (100μmol m(-2) sec(-1)), whereas in the dark, a high mortality rate was found. Uptake of inorganic(14)C into an acid-stable fraction indicated thatOchromonas had a functional photosynthetic apparatus. Heterotrophic growth in both liquid medium and medium containing bacteria was rapid. The maximum growth rate corresponded to a generation time of 5.3 hours. Light had no effect on heterotrophic growth. Cells pregrown onEscherichia coli minicells survived without additional bacteria as food when kept in the light, but rapid death occurred in darkness. In conclusion, heterotrophy is the major mechanism to support growth in this species ofOchromonas, but under poor environmental conditions photoautotrophy might be a strategy for survival rather than growth.

Intact Soil-Core Microcosms for Evaluating the Fate and Ecological Impact of the Release of Genetically Engineered Microorganisms

Intact soil-core microcosms were studied to determine their applicability for evaluating the transport, survival, and potential ecosystem effects of genetically engineered microorganisms before they are released into the environment. Soil-core microcosms were planted with wheat and maize seeds and inoculated with Azospirillum lipoferum SpBr17 and SpRG20a Tn 5 mutants, respectively. Microcosm leachate, rhizosphere soil, plant endorhizosphere, insects, and xylem exudate were sampled for A. lipoferum Tn 5 mutant populations. A. lipoferum Tn 5 populations, determined by most-probable-number technique-DNA hybridization, varied from below detection to 10 6 g of dry root −1 in the rhizosphere, with smaller populations detected in the endorhizosphere. Intact soil-core microcosms were found to maintain some of the complexities of the natural ecosystem and should be particularly useful for initial evaluations of the fate of plant-associated genetically engineered bacteria.

Enumeration of Tn5 mutant bacteria in soil by using a most- probable-number-DNA hybridization procedure and antibiotic resistance

Investigations were made into the utility of DNA hybridization in conjunction with a microdilution most-probable-number procedure for the enumeration of Rhizobium spp. and Pseudomonas putida in soil. Isolates of Rhizobium spp. and P. putida carrying the transposon Tn5 were added to sterile and nonsterile Burbank sandy loam soil and enumerated over time. Soil populations of rhizobia were enumerated by colony hybridization, most-probable-number-DNA hybridization procedure, plate counts, plant infectivity most probable number, and fluorescent antibody counts. Population values compared well for all methods at 5 and 30 days after the addition of cells, although the fluorescent antibody method tended to overestimate the viable population. In nonsterile soil, most-probable-number-DNA hybridization procedure enumerated as few as 10 P. putida Tn5 cells g of soil-1 and 100 R. leguminosarum bv. phaseoli Tn5 cells g of soil-1 and should have utility for following the fate of genetically engineered microorganisms released to the environment. Among the Kmr isolates containing Tn5, approximately 5% gave a dark, more intense autoradiograph when probed with 32P-labeled pGS9 DNA, which facilitated their detection in soil. Hybridization with a pCU101 probe (pGS9 without Tn5) indicated that donor plasmid sequences were being maintained in the bacterial chromosome. Transposon-associated antibiotic resistance was also utilized as a phenotypic marker. Tn5 vector-integrate mutants were successfully enumerated at low populations (10 to 100 cells g of soil-1) in soil by both phenotypic (Kmr) and genotypic (DNA probe) analysis. However, determination of the stability of Tn5 or Tn5 and vector sequences in the bacteria is necessary.

Microbially mediated growth suppression and death of salmonella in composted sewage sludge

The role of compost microflora in the suppression of salmonella regrowth in composted sewage sludge was investigated. Microbial inhibition studies of salmonella growth were conducted on nutrient agar, in composts that had been subjected to different temperatures in compost piles, and in radiation sterilized composts inoculated with selected fractions of the compost microflora. Agar assays of inhibition indicated that bacteria and actinomycetes were not suppressive to salmonellae, but a few fungi were. However, compost inoculation assays showed consistently that fungi were not suppressive, but bacteria and actinomycetes were. In compost inoculation assays, microbial antagonists, when present, either killed salmonellae or reduced their growth rate. No suppression of salmonellae occurred in compost taken from 70°C compost-pile zones despite the presence and growth of many types of microbes. With greater numbers and kinds of microbes in 55°C compost, salmonella growth was suppressed 100-10,000-fold. Salmonellae died when inoculated into compost from unheated zones (25-40°C) of piles. Prior colonization of compost with only noncoliform gram-negative bacteria suppressed salmonellae growth 3,000-fold. Coliforms when inoculated prior to salmonellae accounted for 75% of salmonella die-off. Mesophilic curing to allow colonization of curing piles in their entirety by gram-negative bacteria, especially coliforms, should be an effective way to prevent repopulation by salmonellae.

Naphthalene biodegradation in environmental microcosms: estimates of degradation rates and characterization of metabolites

Naphthalene biodegradation was investigated in microcosms containing sediment and water collected from three ecosystems which varied in past exposure to anthropogenic and petrogenic chemicals. Mineralization half-lives for naphthalene in microcosms ranged from 2.4 weeks in sediment chronically exposed to petroleum hydrocarbons to 4.4 weeks in sediment from a pristine environment. Microbiological analysis of sediments indicated that hydrocarbon-utilizing microbial populations also varied among ecosystems and were 5 to 12 times greater in sediment after chronic petrogenic chemical exposure than in sediment from an uncontaminated ecosystem. Sediment from an ecosystem exposed to agricultural chemicals had a mineralization half-life of 3.2 weeks for naphthalene and showed about a 30-fold increase in heterotrophic bacterial populations in comparison to uncontaminated sediments, but only a 2- to 3-fold increase in hydrocarbon-degrading bacteria. Analysis of organic solvent-extractable residues from the microcosms by high-pressure liquid chromatography detected polar metabolites which accounted for 1 to 3% of the total radioactivity. Purification of these residues by thin-layer chromatography and further analysis by gas chromatography-mass spectrometry indicated that cis-1,2-dihydroxy-1,2-dihydronaphthalene, 1-naphthol, salicylic acid, and catechol were metabolites of naphthalene. These results provide useful estimates for the rates of naphthalene mineralization in different natural ecosystems and on the degradative pathway for microbial metabolism of naphthalene in freshwater and estuarine environments.

Biodegradation of tert-butylphenyl diphenyl phosphate

The biodegradation of tert-butylphenyl diphenyl phosphate (BPDP) was examined in microcosms containing sediment and water from five different ecosystems as part of our studies to elucidate the environmental fate of phosphate ester flame retardants. Biodegradation of [14C]BPDP was monitored in the environmental microcosms by measuring the evolution of 14CO2. Over 37% of BPDP was mineralized after 8 weeks in microcosms from an ecosystem which had chronic exposure to agricultural chemicals. In contrast, only 1.7% of BPDP was degraded to 14CO2 in samples collected from a noncontaminated site. The exposure concentration of BPDP affected the percentage which was degraded to 14CO2 in microcosms from the two most active ecosystems. Mineralization was highest at a concentration of 0.1 mg of BPDP and was inhibited with 10- and 100-fold higher concentrations of BPDP in these microcosms. Indigenous heterotrophic and BPDP-utilizing microbial populations and phosphoesterase enzyme activities were highest in sediments which had the highest biodegradation of BPDP. We observed adaptive increases in both microbial populations and phosphoesterase enzymes in some sediments acclimated to BPDP. Chemical analyses of the residues in the microcosms indicated undegraded BPDP and minor amounts of phenol, tert-butylphenol, diphenyl phosphate, and triphenyl phosphate as biodegradation products. These data suggest that the microbial degradation of BPDP results from at least three catabolic processes and is highest when low concentrations of BPDP are exposed to sediment microorganisms of eutrophic ecosystems which have high phosphotri- and diesterase activities and previous exposure to anthropogenic chemicals.

Microtechnique for isolating fecal coliforms from soil

A most-probable-number microtitration technique for isolating fecal coliforms from soil was developed. A correlation coefficient of 0.86, with a 95% confidence interval of 0.76 less than zeta less than 0.92, was obtained when this technique was compared with the standard elevated-temperature fecal coliform most-probable-number procedure.

Nitrous Oxide Production by Organisms Other than Nitrifiers or Denitrifiers

Heterotrophic bacteria, yeasts, fungi, plants, and animal breath were investigated as possible sources of N 2 O. Microbes found to produce N 2 O from NO 3 − but not consume it were: (i) all of the nitrate-respiring bacteria examined, including strains of Escherichia, Serratia, Klebsiella, Enterobacter, Erwinia , and Bacillus ; (ii) one of the assimilatory nitrate-reducing bacteria examined, Azotobacter vinelandii , but not Azotobacter macrocytogenes or Acinetobacter sp.; and (iii) some but not all of the assimilatory nitrate-reducing yeasts and fungi, including strains of Hansenula, Rhodotorula, Aspergillus, Alternaria , and Fusarium . The NO 3 − -reducing obligate anaerobe Clostridium KDHS2 did not produce N 2 O. Production of N 2 O occurred only in stationary phase. The nitrate-respiring bacteria produced much more N 2 O than the other organisms, with yields of N 2 O ranging from 3 to 36% of 3.5 mM NO 3 − . Production of N 2 O was apparently not regulated by ammonium and was not restricted to aerobic or anaerobic conditions. Plants do not appear to produce N 2 O, although N 2 O was found to arise from some damaged plant tops, probably due to microbial growth. Concentrations of N 2 O above the ambient level in the atmosphere were found in human breath and appeared to increase after a meal of high-nitrate food.

Bacteria on closed-boll and commercially harvested cotton

The bacterial content of specially treated cottons used by other investigators to test human pulmonary responses to cotton dust was examined. Cotton from Lubbock, Tex. and Stoneville, Miss. were either (i) harvested by machine and handled as commercial bale cotton, (ii) harvested as closed bolls with bracts intact and opened under special conditions, (iii) harvested as closed bolls, with bracts being removed and opened under special conditions, or (iv) harvested by (stoneville only). Bacillus spp. were isolated from all samples and predominated in cotton from Stoneville. Enterobacter agglomerans was isolated from all but one sample, the Stoneville closed-boll bract-removed cotton, and predominated in Lubbock samples. Aerogenic and anaerogenic biogroups of E. agglomerans were isolated; only aerogenic strain b of E. agglomerans was present in samples from both locations. Klebsiella ozaenae and K. pneumoniae were isolated only from Lubbock samples. Cotton from Lubbock yielded 100 to 1,000 times more bacteria, both total and gram negative, than did comparably treated cotton from Stoneville. Thus, differences in growing and processing conditions at the two locations were associated with large differences in the bacterial content of the cotton, but harvesting green bolls and removing bracts had little effect. The bacterial content of Stoneville washed cotton, and it paralleled the differences reported (Boehlecke et al., Am. Rev. Respir, Dis. 123:152, 1981) in pulmonary function responses when subjects were exposed to dust (0.6 mg/m3) from these two cottons. Levels of gram-negative and total bacteria on all samples were comparable to those previously reported for field-weathered cottons from various locations throughout the world.

Estimation of the most probable number with a programable pocket calculator

The most-probable-number method has many potential applications, particularly if many tubes per dilution and many dilution levels are used. Increasing the number of cultures is possible with modern automatic and semiautomatic equipment. However, available tables are not sufficiently detailed to handle data from a large number of culture tubes used in an assay. This paper provides a computer program capable of handling the necessary arithmetic and written for a hand-held, advanced programable calculator.

Nitrogen conservation in a tropical rain forest

A series of plots in an Amazonian Rain Forest were trenched and treated with calcium to determine the effects of perturbation on numbers and activity of nitrifying bacteria. Although treatment resulted in between 2 and 26% of the nitrogen being lost from the humus layer, virtually all of it was in the NH ₄⁺ form. Numbers of nitrifying bacteria in the plots were relatively low. The low numbers and low activity of nitrifying bacteria is attributed to the low pH and high concentration of tannins in the root mat. It is hypothesized that the suppression of nitrifying bacteria results in nitrogen conservation in the rain forest.