Validation of microbial community structure and ecological functional parameters in an aquatic microcosm designed for testing genetically engineered microorganisms

Microcosms were designed to facilitate studies of the fate, functioning, and ecological effects of microorganisms released into the aquatic environment. The microcosms were three-phase systems (sediment/water/air) with three compartments (a primary producer component, a herbivore grazer component, and intact sediment cores). The microcosms were validated by comparing gross ecological parameters and microbial community structure between the microcosms and the eutrophic Lake Bagsværd, which was simulated in the model. The photosynthetic potential and chlorophyll a concentrations were significantly lower in the microcosms than in the lake, which apparently was due to inorganic nutrient limitation. In the microcosms, total bacterial numbers and metabolic activity by [³H]thymidine incorporation were unaffected by the reduced algal biomass and primary production, simulating field conditions closely, with a strong dependence on temperature. Two days after filling the microcosms, the percentage of similarity of the microbial communities in the microcosm and Lake Bagsværd was 40%, measured by hybridizations of total microbial DNA. The similarity increased during the 10-day experimental period to 63–76%. In two experiments, Alcaligenes eutrophus AEO106(pRO101) was released into the microcosms. The release reduced the similarity between microcosms and lake to 2% and 27%, depending on the number of introduced cells. Concomitant to a decline in the A. eutrophus AEO106(pRO101) population, the similarity gradually recovered. It is concluded that the microcosms can simulate a freshwater lake ecosystem, but care has to be taken when extrapolating microcosm results to the source ecosystem because of the possible different selective conditions in the microcosm.     

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.     

The fate of a genetically modified Pseudomonas strain and its transgene during the composting of poultry manure

The fate of the genetically modified (GM) Pseudomonas chlororaphis strain 3732 RN-L11 and its transgene (lacZ insert) during composting of chicken manure was studied using plate count and nested polymerase chain reaction (PCR) methods. The detection sensitivity of the nested PCR method was 165 copies of the modified gene per gram of moist compost or soil. Compost microcosms consisted of a 100-g mixture of chicken manure and peat, whereas soil microcosms were 100-g samples of sandy clay loam. Each microcosm was inoculated with 4 x 1010 CFU of P. chlororaphis RN-L11. In controlled temperature studies, neither P. chlororaphis RN-L11 nor its transgene could be detected in compost microcosms after incubation temperature was elevated to 45 degrees C or above for one or more days. In contrast, in the compost microcosms incubated at 23 degrees C, the target organism was not detected by the plate count method after 6 days, but its transgene was detectable for at least 45 days. In compost bins, the target organism was not recovered from compost microcosms or soil microcosms at different levels in the bins for 29 days. However, the transgene was detected in 8 of the 9 soil microcosms and in only 1 of the 9 compost microcosms. The compost microcosm in which transgene was detected was at the lower level of the bin where temperatures remained below 45 degrees C. The findings indicated that composting of organic wastes could be used to reduce or degrade heat sensitive GM microorganisms and their transgenes.     

Application of carbon source utilization patterns to measure the metabolic similarity of complex dental plaque biofilm microcosms

Biolog technology was applied to measure the metabolic similarity of plaque biofilm microcosms, which model the complex properties of dental plaque in vivo. The choice of Biolog plate, incubation time, and incubation conditions strongly influenced utilization profiles. For plaque biofilm microcosms, Biolog GP2 plates incubated anaerobically in an H2-free atmosphere gave the clearest profile. To test the application of the Biolog GP2 assay, plaque microcosms were developed under different nutrient conditions in which the frequency of sucrose application was varied. Cluster analysis of Biolog GP2 data from 10 microcosm biofilms correlated with sucrose frequency. Aciduric bacteria (Streptococcus mutans plus lactobacilli) predominated in the plaques receiving high-frequency sucrose applications. Agreement between the Biolog GP2 groupings with nutrient and compositional changes suggests that Biolog analysis is a valuable technique for analyzing the metabolic similarity of dental plaque biofilm microcosms and other high-nutrient or predominantly anaerobic ecosystems.     

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.     

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

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

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

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

Symbiotic germination and development of myco-heterotrophic plants in nature: transfer of carbon from ectomycorrhizal Salix repens and Betula pendula to the orchid Corallorhiza trifida through shared hyphal connections

Seedlings of the myco-heterotrophic orchid Corallorhiza trifida which had been germinated in the field in mesh bags developed hyphal links and mycorrhizas with Betula pendula and Salix repens , but not with Pinus sylvestris , when transplanted into soil microcosms. The fungus connecting the myco-heterotroph to Betula and Salix formed endomycorrhiza in the orchid with typical pelotons, but formed ectomycorrhizas with the autotrophs. The orchid plants, when linked to Betula and Salix by fungal hyphae, gained 6–14% in weight over 25–28 wk. In microcosms supporting P. sylvestris , and in control microcosms which lacked autotrophs, the Corallorhiza plants lost 13% of their weight over the same period. In the course of the 28-wk experimental period new Corallorhiza seedlings, in addition to those added as part of the experiment, appeared in the microcosms containing Salix and Betula but not in the Pinus microcosms. Shoots of Betula and Salix plants grown in association with Corallorhiza were fed with ¹⁴CO₂, and the movement of the isotope was subsequently traced by a combination of digital autoradiography and tissue oxidation. Direct transfer of C from both autotrophs to the myco-heterotroph occurred in all cases where the associates had become connected by a shared fungal symbiont. Orchid seedlings lacking these hyphal connections, introduced to the microcosms as controls immediately before isotope feeding, failed to assimilate significant amounts of C. The results provide the first experimental confirmation that growth of Corallorhiza trifida can be sustained by supply of C received directly from an autotrophic partner through linked fungal mycelia.     

Application of Carbon Source Utilization Patterns To Measure the Metabolic Similarity of Complex Dental Plaque Biofilm Microcosms

Biolog technology was applied to measure the metabolic similarity of plaque biofilm microcosms, which model the complex properties of dental plaque in vivo. The choice of Biolog plate, incubation time, and incubation conditions strongly influenced utilization profiles. For plaque biofilm microcosms, Biolog GP2 plates incubated anaerobically in an H₂-free atmosphere gave the clearest profile. To test the application of the Biolog GP2 assay, plaque microcosms were developed under different nutrient conditions in which the frequency of sucrose application was varied. Cluster analysis of Biolog GP2 data from 10 microcosm biofilms correlated with sucrose frequency. Aciduric bacteria (Streptococcus mutans plus lactobacilli) predominated in the plaques receiving high-frequency sucrose applications. Agreement between the Biolog GP2 groupings with nutrient and compositional changes suggests that Biolog analysis is a valuable technique for analyzing the metabolic similarity of dental plaque biofilm microcosms and other high-nutrient or predominantly anaerobic ecosystems.     

Effects of flooding on leaf litter decomposition in microcosms

Summary The effects of hydroperiod on decomposition rates of senescent Acer rubrum leaves were tested in microcosms in a controlled laboratory environment. Microcosm treatments included continuously flooded, continuously unflooded, and fluctuating hydroperiods. All flooding treatments promoted decomposition but variations in hydroperiod had no significant effects. A leaching experiment indicated the higher decay rates under flooded conditions were primarily due to high leaching losses from soaking. Unlike nutrient dynamics in the field, where net accumulation occurs, nitrogen and phosphorus in the litter in the microcosms exhibited net losses. The major external inputs which provide a source of nitrogen and phosphorus for immobilization in the field were lacking in the microcosms. Calcium, magnesium, and potassium exhibited net losses except for calcium in the unflooded microcosms. The microcosm results demonstrated the importance of external inputs to litter nutrient relations.     

罗非鱼对微型生态系统浮游生物群落和初级生产力的影响

本文报道罗非鱼不同放养密度对淡水微型生态系统结构与功能影响的部分研究结果。罗非鱼的捕食使微型生态系统中浮游动物密度下降,引起浮游植物密度、初级生产力和P/R系数的增长,同时使水柱透明度降低而pH值增高,以致于实验后期微型生态系统具有典型的富营养化水体的特征。就罗非鱼放养密度不同的微型生态系统而言,虽然其浮游生物密度和P/R系数存在显著的组(或部分组)间差异,但不同密度组的初级生产力水平和最终的理化状况相差不大,并且罗非鱼的收获量甚为接近。因此,实验条件下微型生态系统的群落结构和代谢的变化,按照营养级联假说不能很好地予以解释,表明微型生态系统是由捕食(下行影响)和理化因素(上行影响)共同调节或控制的。根据微型生态系统的实验结果推断,放养较大密度的罗非鱼,将会加速营养物负荷较高的天然水域富营养化的进程。     

Enrichment of cadmium-mediated antibiotic-resistant bacteria in a Douglas-fir (Pseudotsuga menziesii) litter microcosm.

A set of Douglas-fir needle litter microcosms was amended with cadmium, acid, a combination of both, or neither. After 2 weeks of incubation, bacterial colony counts were made of litter homogenates inoculated onto agar media containing an antibiotic (streptomycin, chloromycetin, ampicillin, or gentamicin), cadmium, both, or neither. In all microcosms bacterial abundance was similar but the quality was very dissimiliar. Cadmium-treated microcosms had populations enriched for cadmium and gentamicin resistance and streptomycin and chloramphenicol sensitivity. Acid amendment had no consistent effect on the microcosm populations except that which could be attributed to the cadmium treatment amendment alone.     

Involvement of a chlorobenzoate-catabolic transposon, Tn5271, in community adaptation to chlorobiphenyl, chloroaniline, and 2,4-dichlorophenoxyacetic acid in a freshwater ecosystem.

A chlorobenzoate-catabolic transposon (Tn5271) was introduced on a conjugative plasmid (pBRC60) in the natural host, Alcaligenes sp. strain BR60, into lake water and sediment flowthrough microcosms. Experimental microcosms were exposed to micromolar levels of 3-chlorobenzoate, 4-chloroaniline, 2,4-dichlorophenoxyacetate, or 3-chlorobiphenyl. The populations of the host, BR60, and organisms carrying Tn5271 were monitored over a 100-day period by use of selective plate counts and the most-probable-number-DNA hybridization method. Populations of Tn5271-carrying bacteria were significantly higher in microcosms dosed with 3-chlorobenzoate, 4-chloroaniline, and 3-chlorobiphenyl than in the control microcosms, indicating that each of these chemicals exerts a selective force on this particular genotype in natural systems. The rates of 3-chlorobenzoate uptake and respiration correlated with Tn5271-carrying populations, as did the rates of 4-chloroaniline uptake and respiration. Plasmid transfer in the 3-chlorobenzoate- and 3-chlorobiphenyl-dosed microcosms resulted in the selection of three phenotypic clusters of chlorobenzoate degraders, only one of which was closely related to the original pBRC60 (Tn5271) donor, Alcaligenes sp. strain BR60. Bacteria dominating 4-chloroaniline-dosed microcosms carried IS1071, the class II insertion sequence that brackets Tn5271, on a plasmid unrelated to pBRC60. The importance of plasmid transfer and transposition during chemical adaptation is discussed.     

Enrichment of cadmium-mediated antibiotic-resistant bacteria in a Douglas-fir (Pseudotsuga menziesii) litter microcosm.

A set of Douglas-fir needle litter microcosms was amended with cadmium, acid, a combination of both, or neither. After 2 weeks of incubation, bacterial colony counts were made of litter homogenates inoculated onto agar media containing an antibiotic (streptomycin, chloromycetin, ampicillin, or gentamicin), cadmium, both, or neither. In all microcosms bacterial abundance was similar but the quality was very dissimiliar. Cadmium-treated microcosms had populations enriched for cadmium and gentamicin resistance and streptomycin and chloramphenicol sensitivity. Acid amendment had no consistent effect on the microcosm populations except that which could be attributed to the cadmium treatment amendment alone.     

Bioaugmentation of butane-utilizing microorganisms to promote cometabolism of 1,1,1-trichloroethane in groundwater microcosms

The transformation of 1,1,1-trichloroethane (1,1,1-TCA) in ioaugmented and non-augmented microcosms was evaluated. The microcosms contained roundwater and aquifer materials from a test site at Moffett Field, Sunnyvale, CA. The initial inoculum for bioaugmentation was a butane-utilizing enrichment from the subsurface of the Hanford DOE site. The non-augmented microcosm required 80 days of incubation before butane-utilization was observed while the augmented microcosms required 3 days. Initially the augmented microcosms were effective in transforming 1,1,1-TCA, but their transformation ability decreased after prolonged incubation. The non-augmented microcosms initially showed limited 1,1,1-TCA transformation but improved with time. After 440 days, both the non-augmented and augmented microcosms had similar transformation yields (0.04 mg 1,1,1-TCA/mg butane) and had similar microbial composition (DNA fingerprints). Subsequent microcosms, when bioaugmented with a Hanford enrichment that was repeatedly grown in 100% mineral media, did not effectively grow or transform 1,1,1-TCA under groundwater nutrient conditions. Microcosm tests to study the effect of mineral media on transformation ability were performed with the Hanford enrichment. Microcosms with 50% mineral media in groundwater most effectively utilized butane and transformed 1,1,1-TCA, while microcosms with groundwater only and microcosms with 5% mineral media in groundwater lost their 1,1,1-TCA transformation ability. DNA fingerprinting indicated shifts in the microbial composition with the different mineral media combinations. Successful bioaugmentation was achieved by enriching butane-utilizers from Moffett Field microcosms that were effective in groundwater with no mineral media added. The results suggest that successful in-situ bioaugmentation might be achieved through the addition of enriched cultures that perform well under subsurface nutrient conditions.     

Transport of a genetically engineered Pseudomonas fluorescens strain through a soil microcosm.

Vertical soil microcosms flushed with groundwater were used to study the influence of water movement on survival and transport of a genetically engineered Pseudomonas fluorescens C5t strain through a loamy sand and a loam soil. Transport of cells introduced into the top 1 cm of the vertical soil microcosms was dependent on the flow rate of water and the number of times microcosms were flushed with groundwater. The presence of wheat roots growing downward in the microcosms contributed only slightly to the movement of P. fluorescens C5t cells to lower soil regions of the loamy sand microcosms, but enhanced downward transport in the loam microcosms. Furthermore, the introduced P. fluorescens C5t cells were detected in the effluent water samples even after three flushes of groundwater and 10 days of incubation. As evidenced by a comparison of counts from immunofluorescence and selective plating, nonculturable C5t cells occurred in day 10 soil and percolated water samples, primarily of the loamy sand microcosms. Vertical soil microcosms that use water movement may be useful in studying the survival and transport of genetically engineered bacteria in soil under a variety of conditions prior to field testing.     

Introduction of anaerobic dechlorinating bacteria into soil slurry microcosms and nested-PCR monitoring.

Desulfomonile tiedjei and Desulfitobacterium dehalogenans were chosen as model bacteria to demonstrate the introduction of an anaerobic microbia reductive dechlorination activity into nonsterile soil slurry microcosms by inoculation. De novo 3-chlorobenzoate dechlorination activity was established with the bacterium D. tiedjei in microcosms normally devoid of this dechlorination capacity. The addition of D. tiedjei to microcosms supplemented with 20 mM pyruvate as the cosubstrate resulted in total biotransformation of 1.5 mM 3-chlorobenzoate within 7 days. The introduction of the bacterium Desulfitobacterium dehalogenans into nonsterile microcosms resulted in a shortening of the period required for dechlorination activity to be established. In microcosms inoculated with Desulfitobacterium dehalogenans, total degradation of 6 mM 3-chloro-4-hydroxy phenoxyacetic acid (3-Cl-4-OHPA) was observed after 4 days in contrast to the result in noninoculated microcosms, where the total degradation of 3-Cl-4-OHPA by indigenous microorganisms was observed after 11 days. Both externally introduced bacterial strains were detected in soil slurry microcosms by a nested-PCR methodology.     

Transport of a genetically engineered Pseudomonas fluorescens strain through a soil microcosm

Vertical soil microcosms flushed with groundwater were used to study the influence of water movement on survival and transport of a genetically engineered Pseudomonas fluorescens C5t strain through a loamy sand and a loam soil. Transport of cells introduced into the top 1 cm of the vertical soil microcosms was dependent on the flow rate of water and the number of times microcosms were flushed with groundwater. The presence of wheat roots growing downward in the microcosms contributed only slightly to the movement of P. fluorescens C5t cells to lower soil regions of the loamy sand microcosms, but enhanced downward transport in the loam microcosms. Furthermore, the introduced P. fluorescens C5t cells were detected in the effluent water samples even after three flushes of groundwater and 10 days of incubation. As evidenced by a comparison of counts from immunofluorescence and selective plating, nonculturable C5t cells occurred in day 10 soil and percolated water samples, primarily of the loamy sand microcosms. Vertical soil microcosms that use water movement may be useful in studying the survival and transport of genetically engineered bacteria in soil under a variety of conditions prior to field testing.     

Fatty acid-oxidizing consortia along a nutrient gradient in the Florida Everglades

The Florida Everglades is one of the largest freshwater marshes in North America and has been subject to eutrophication for decades. A gradient in P concentrations extends for several kilometers into the interior of the northern regions of the marsh, and the structure and function of soil microbial communities vary along the gradient. In this study, stable isotope probing was employed to investigate the fate of carbon from the fermentation products propionate and butyrate in soils from three sites along the nutrient gradient. For propionate microcosms, 16S rRNA gene clone libraries from eutrophic and transition sites were dominated by sequences related to previously described propionate oxidizers, such as Pelotomaculum spp. and Syntrophobacter spp. Significant representation was also observed for sequences related to Smithella propionica, which dismutates propionate to butyrate. Sequences of dominant phylotypes from oligotrophic samples did not cluster with known syntrophs but with sulfate-reducing prokaryotes (SRP) and Pelobacter spp. In butyrate microcosms, sequences clustering with Syntrophospora spp. and Syntrophomonas spp. dominated eutrophic microcosms, and sequences related to Pelospora dominated the transition microcosm. Sequences related to Pelospora spp. and SRP dominated clone libraries from oligotrophic microcosms. Sequences from diverse bacterial phyla and primary fermenters were also present in most libraries. Archaeal sequences from eutrophic microcosms included sequences characteristic of Methanomicrobiaceae, Methanospirillaceae, and Methanosaetaceae. Oligotrophic microcosms were dominated by acetotrophs, including sequences related to Methanosarcina, suggesting accumulation of acetate.     

微型生态系统中正磷酸盐的周转时间的估算

在考查罗非鱼或鲢、鳙下行影响的微型生态系统实验后期,以水柱正磷酸盐(PO4-P)完全被浮游植物摄取所需要的时间为指标,估算了系统中PO4-P的周转时间,其中浮游植物的PO4-P摄取率是采用挂瓶法来测定和估算的。结果表明,两组实验中大多数有鱼系统的浮游植物PO4-P摄取率都显着地比无鱼系统高,而PO4-P周转时间的估算值均最着地小于无鱼系统。经相关分析测定,两组实验中浮游植物的PO4-P摄取率皆显着地正相关于浮游植物密度和初级生产力,同水柱PO4-P浓度之间的负相关关系则不显着。根据估算结果看来,罗非鱼对系统中磷循环速率的影响比鲢、鳙大得多,而鳙的影响又明显地大于鲢。这些鱼类使微型生态系统中PO4-P的周转时间缩短,可能主要是它们加速了系统中PO4-P再生的结果。