Monitoring the diversity of Rhizobium meliloti field and microcosm isolates with a novel rapid genotyping method using insertion elements

Rhizobium meliloti strains isolated from alfalfa plants grown in a mining recultivation field, in a model ecosystem (microcosm) and in soil core containers were characterized by two new taxonomic methods, fingerprinting and handprinting, using insertion sequence elements (IS) as hybridization probes. The diversity of strains within the field population could first be detected with IS-fingerprinting, whereby nearly three times more groups of Rhizobium meliloti strains could be identified in comparison to the groups according to plasmid profiles. This complexity and diversity of the rhizobial population was also detected in microcosm studies. Strains identified among the field population were also detected in the microcosm studies. The persistence of rhizobia in soil was demonstrated in soil core samples held in a cold room for 2 years. A decrease in the genomic diversity of the R. meliloti population upon soil storage was observed. A novel monitoring method, IS-handprinting, in which the presence of certain endogenous insertion elements within a strain is registered, was successfully employed to characterize genetically the field R. meliloti strains with simplicity and speed. In contrast to IS-fingerprinting, IS-handprinting is based on a simple plus-or-minus detection, which is sufficient for a taxonomic characterization. Both methods, using a non-radioactive detection system, are sensitive enough to detect one copy of an insertion element in a strain's genome. IS-fingerprinting, with its fine resolution, would be suitable for ecological studies of individual strains in any complex ecosystem, whereas IS-handprinting would be suitable for monitoring strains and characterizing large numbers of strains.     

Survival of Bacillus licheniformis in Seawater Model Ecosystems

The fate of Bacillus licheniformis DSM 13 was monitored after introduction into laboratory microcosms and mesocosms established in the Knebel Vig estuary, Denmark. The model organism was detected by a combination of immunofluorescence microscopy and nonselective plating followed by colony blotting. This allowed simultaneous quantification of intact cells and culturable cells. B. licheniformis DSM 13 adapted poorly to the conditions in filtered (0.2-μm-pore-size filter) seawater. Results from additional microcosm studies using natural seawater demonstrated that protozoan grazing also was important in regulating the population of the introduced model organism. In experiments using mesocosms, B. licheniformis DSM 13 also showed a rapid die-off. The introduction of the organism led to increased nutrient levels and to increased growth of both autotrophic and heterotrophic components of the plankton community compared with those of control enclosures. Thereby, a more intensive predation impact on the bacterioplankton community was induced. The combination of microcosm and mesocosm experiments provides a scenario in which the influence of single biotic and abiotic factors on survival of introduced organisms can be tested and in which the effect of the introduction on ecosystem structure and function can be evaluated. This test concept might prove useful in risk assessment of genetically modified microorganisms.     

Micro-environmental factors and the endemism of bromeliad aquatic fauna

Tank bromeliads harbour aquatic microcosms with many endemic species among their leaves. We performed a set of experiments to determine which factors maintain the bromeliad aquatic fauna in isolation from neighbouring ponds. We cultivated three invertebrates species (an ostracod, an annelid and a cladoceran) from a pond surrounded by terrestrial bromeliads in Southeastern Brazil and introduced them inside cleaned bromeliads, using recipients with the same volume as controls. The pH, conductivity and organism densities were monitored in the bromeliad samples and controls for 41 days. The samples introduced inside the cleaned bromeliads showed a significant decrease in pH and conductivity compared to the controls. The pond organism populations introduced in the bromeliads presented a high extinction rate and a significant population decrease when compared to the ones introduced in the controls. We attributed the population decline experienced by the pond organisms to the oligotrophic conditions generated inside the tanks by the bromeliads due to the nutrient absorption. We suggest that the changes in water chemistry induced by the bromeliads could play an important role in isolating their microcosm communities from other freshwater systems. Other mechanisms that could produce the high rates of endemism in bromeliad fauna are discussed. Handling editor: K. Martens     

Gene transfer of Alcaligenes eutrophus JMP134 plasmid pJP4 to indigenous soil recipients.

This study evaluated the potential for gene transfer of a large catabolic plasmid from an introduced organism to indigenous soil recipients. The donor organism Alcaligenes eutrophus JMP134 contained the 80-kb plasmid pJP4, which contains genes that code for mercury resistance. Genes on this plasmid plus chromosomal genes also allow degradation of 2,4-dichloruphenoxyacetic acid (2,4-D). When JMP134 was inoculated into a nonsterile soil microcosm amended with 1,000 micrograms of 2,4-D g-1, significant (10(6) g of soil-1) populations of indigenous recipients or transconjugants arose. These transconjugants all contained an 80-kb plasmid similar in size to pJP4, and all degraded 2,4-D. In addition, all transconjugants were resistant to mercury and contained the tfdB gene of pJP4 as detected by PCR. No mercury-resistant, 2,4-D-degrading organisms with large plasmids or the tfdB gene were found in the 2,4-D-amended but uninoculated control microcosm. These data clearly show that the plasmid pJP4 was transferred to indigenous soil recipients. Even more striking is the fact that not only did the indigenous transconjugant population survive and proliferate but also enhanced rates of 2,4-D degradation occurred relative to microcosms in which no such gene transfer occurred. Overall, these data indicate that gene transfer from introduced organisms is an effective means of bioaugmentation and that survival of the introduced organism is not a prerequisite for biodegradation that utilizes introduced biodegradative genes.     

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.     

Validation of Microcosms for Examining the Survival of Pseudomonas aureofaciens (lacZY) in Soil

Evaluating the safety and efficacy of a recombinant bacterium prior to its release into the terrestrial environment requires that risk assessment data be collected in the laboratory. Much of this information is obtained with the use of microcosms. The design of the microcosm significantly affects the ability of the recombinant microorganism to survive in soil and, thus, complicates the risk assessment process. To standardize microcosms for future use, we evaluated the survival of Pseudomonas aureofaciens 3732 RN-L11 (lacZY Rif(supr) Nal(supr)) in intact soil cores (5.0 by 15 cm; polyvinyl chloride core) and disturbed soil microcosms (50 g of fresh, sieved soil). Survival data were compared with those obtained during a field release. The intact soil core microcosm was shown to closely simulate results obtained in the field. The intact soil core microcosm closely predicts survival in bulk soil and in the rhizosphere of wheat. Data obtained with the microcosm were also similar when evaluated in separate studies in two different years. In 1993, P. aureofaciens survived for approximately 63 days in bulk soil and 96 days in the rhizosphere. The disturbed soil microcosm exhibited a much more rapid decline in population size (34 days to zero) than the intact core microcosm. We speculate that drying and sieving of soil for the disturbed soil microcosm affected the ability of the soil to support the survival of P. aureofaciens. These results demonstrate that a small, inexpensive, and simple intact soil core microcosm may be appropriate for risk assessment.     

Laboratory culture conditions affect stability of resistance to Bacillus thuringiensis Cry1Ac in Plutella xylostella (Lep., Plutellidae)

Abstract:  Populations of Plutella xylostella L. with high (laboratory re-selected) and low levels (unselected) of resistance to the Bacillus thuringiensis ( B.t. ) toxin Cry1Ac were maintained under controlled environment conditions in the absence of any further selection pressure. Larvae were maintained either in discrete generations on freshly excised leaves replaced ad lib (standard culture system) or in microcosm cages holding up to 12 potted Chinese cabbage plants, allowing progressively overlapping generations of insects. After 12 generations in the microcosm cages, the LC₅₀ values of both selected and unselected populations were not significantly different from those of a standard susceptible population. Under standard culture conditions, the LC₅₀ value for unselected insects after 12 generations was almost identical to that of unselected insects in the microcosm cages, whereas the LC₅₀ value for selected insects was 1250-fold greater. The fecundity of the selected population was significantly lower compared with that of the same population in the microcosm cages after 12 generations. There was no significant change in the fecundity of the unselected population after 12 generations in the microcosm cages. The results show, that differences in the culture system (microcosm vs. standard) and in the resistance level (re-selected vs. unselected) can have a marked influence on the stability of resistance to a B.t. toxin in an insect population. Possible factors involved in determining the rate at which resistance declines are discussed.     

Quorum Sensing and Density-Dependent Dispersal in an Aquatic Model System

Many organisms use cues to decide whether to disperse or not, especially those related to the composition of their environment. Dispersal hence sometimes depends on population density, which can be important for the dynamics and evolution of sub-divided populations. But very little is known about the factors that organisms use to inform their dispersal decision. We investigated the cues underlying density-dependent dispersal in inter-connected microcosms of the freshwater protozoan Paramecium caudatum. In two experiments, we manipulated (i) the number of cells per microcosm and (ii) the origin of their culture medium (supernatant from high- or low-density populations). We found a negative relationship between population density and rates of dispersal, suggesting the use of physical cues. There was no significant effect of culture medium origin on dispersal and thus no support for chemical cues usage. These results suggest that the perception of density – and as a result, the decision to disperse – in this organism can be based on physical factors. This type of quorum sensing may be an adaptation optimizing small scale monitoring of the environment and swarm formation in open water.     

Sulfate-Mediated Bacterial Population Shift in a Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX)-Degrading Anaerobic Enrichment Culture

The effects of sulfate on the population dynamics of an anaerobic hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX)-degrading consortium were studied using terminal restriction fragment length polymorphism (T-RFLP) analysis. One hundred percent of the initial RDX was degraded in the sulfate-amended culture within 3 days of incubation. In the sulfate-unamended cultures, 35% of the initial RDX remained after 3 days and 8% after 7 days of incubation. Based on the T-RFLP distribution of the community 16S rDNA genes, the microcosm consisted predominantly of two organisms, a Geobacter sp. (78%) and an Acetobacterium sp. (14%). However, in the presence of sulfate, both species decreased to less than 3% of the total population within 3 days and an unclassified Clostridiaceae became the dominant organism at 40% the total fragment distribution. This indicated the explosive-degrading consortium had greater diversity than initially perceived and rapidly adapted to a readily available electron acceptor, which in turn stimulated RDX degradation.     

Direct and indirect interactions for coexistence in a species-defined microcosm

Mechanisms for coexistence among micro-organisms were studied by using a species-defined microcosm, consisting of the bacterium Escherichia coli, the ciliate Tetrahymena thermophila and the alga Euglena gracilis. These organisms were chosen as representative of ecological functional groups i.e. decomposer, consumer and producer, respectively. Direct and indirect interactions among these organisms were evaluated by comparisons of their population dynamics in culture with different combinations of the three species. There was an E. coli cell density dependent predator–prey interaction between T. thermophila and E. coli which was only established when there were more than 10⁶ cells ml^–1 of E. coli. Indirect interactions were evaluated from the cultivation of each organism in media containing metabolites of the others. Metabolites from each population strongly accelerated the growth of their own populations and those of the others except for the self-toxicity effect of E. coli metabolites. These observations suggested that not only the cell–cell contact of direct interactions, but also metabolite-mediated indirect interactions supported the maintenance of the populations of each micro-organism and their coexistence. In natural ecosystems, there are many interactions and it is difficult to evaluate all those regulating community dynamics. The gnotobiotic microcosm used in this study was shown to be suitable for examining the specific, species–species microbial interactions.     

Tracking the Response of Burkholderia cepacia G4 5223-PR1 in Aquifer Microcosms

The introduction of bacteria into the environment for bioremediation purposes (bioaugmentation) requires analysis and monitoring of microbial population dynamics to define persistence and activity from both efficacy and risk assessment perspectives. Burkholderia cepacia G4 5223-PR1 is a Tn5 insertion mutant which constitutively expresses a toluene ortho-monooxygenase that degrades trichloroethylene (TCE). This ability of G4 5223-PR1 to degrade TCE without aromatic induction may be useful for bioremediation of TCE-containing aquifers and groundwater. Thus, a simulated aquifer sediment system and groundwater microcosms were used to monitor the survival of G4 5223-PR1. The fate of G4 5223-PR1 in sediment was monitored by indirect immunofluorescence microscopy, a colony blot assay, and growth on selective medium. G4 5223-PR1 was detected immunologically by using a highly specific monoclonal antibody which reacted against the O-specific polysaccharide chain of the lipopolysaccharides of this organism. G4 5223-PR1 survived well in sterilized groundwater, although in nonsterile groundwater microcosms rapid decreases in the G4 5223-PR1 cell population were observed. Ten days after inoculation no G4 5223-PR1 cells could be detected by selective plating or immunofluorescence. G4 5223-PR1 survival was greater in a nonsterile aquifer sediment microcosm, although after 22 days of elution the number of G4 5223-PR1 cells was low. Our results demonstrate the utility of monoclonal antibody tracking methods and the importance of biotic interactions in determining the persistence of introduced microorganisms.     

Factors influencing survival of Legionella pneumophila serotype 1 in hot spring water and tap water

The factors involved in the survival of Legionella pneumophila in the microcosms of both hot spring water and tap water were studied by examining cultivability and metabolic activity. L. pneumophila could survive by maintaining metabolic activity but was noncultivable in all microcosms at 42 degrees C, except for one microcosm with a pH of <2.0. Lower temperatures supported survival without loss of cultivability. The cultivability declined with increasing temperature, although metabolic activity was observed at temperatures of up to 45 degrees C. The optimal range of pH for survival was between 6.0 and 8. The metabolic activity could be maintained for long periods even in microcosms with high concentrations of salt. The cultivability of organisms in the post-exponential phase in a tap water microcosm with a low inoculum size was more rapidly reduced than that of organisms in the exponential phase. In contrast, the loss of cultivability in microcosms of a high inoculum size was significant in the exponential phase. Random(ly) amplified polymorphic DNA analysis of microcosms where cultivability was lost but metabolic activity was retained showed no change compared to cells grown freshly, although an effect on the amplified DNA band pattern by production of stress proteins was expected. Resuscitation by the addition of Acanthamoeba castellanii to the microcosm in which cultivability was completely lost but metabolic activity was maintained was observed only in part of the cell population. Our results suggest that L. pneumophila cell populations can potentially survive as free organisms for long periods by maintaining metabolic activity but temporarily losing cultivability under strict environments and requiring resuscitation by ingestion by amoebas.     

Crude oil degradation efficiency of a recombinant Acinetobacter baumannii strain and its survival in crude oil-contaminated soil microcosm

A hydrocarbon degrading Acinetobacter baumannii S30 strain, isolated from crude oil-contaminated soil, was inserted with the lux gene from the luciferase gene cassette luxCDABE. Soil microcosms were designed to study the degradation efficacy for total petroleum hydrocarbon (TPH) of crude oil by lux-tagged A. baumannii S30 pJES. Bioaugmentation of a TPH-contaminated microcosm with A baumannii S30 pJES showed that TPH levels were reduced from 89.3 to 53.9 g/kg soil in 90 days. Biodegradation of TPH by A baumannii S30 pJES was also monitored in shake flask conditions, which showed a reduction of initial TPH levels by over 50% at the end of 120 h. A lux-PCR-based approach along with the standard dilution plating with selective antibiotics was successfully utilized to monitor the survivability of the lux-tagged strain A. baumannii S30 pJES in soil microcosms and stability of the lux insert in the host strain A. baumannii S30. The selective plating technique indicated the population of A. baumannii S30 pJES to be 6.5+/-0.13 x 10(8) CFU/g at day zero (just after bioaugmentation) and 2.09+/-0.08 x 10(8) CFU/g of soil after 90 days of incubation. lux-PCR confirmed the stability of the insert in all the randomly selected colonies of A. baumannii strains from the antibiotic plates. The lux insert was stable after 50 generations in Luria Bertini broth and storage at -70 degrees C as glycerol stocks for over a year. These results revealed that the lux insert was stable and lux-tagged A. baumannii S30 strain could survive in a TPH-contaminated soil microcosm and could degrade TPH in the soil microcosm conditions. It can be used as an effective marker to monitor the survival of augmented strains at a bioremediation site.     

Thalassia testudinum banks ex könig seedling success in a coral reef microcosm

Thalassia seedlings collected in the Bahama Islands were transplanted into the lagoon of a coral reef microcosm where their survival and growth was monitored. Only 25% of the original number planted survived after eight months. The leaves grew a minimum of 2 cm per month. Seedling growth in the microcosm exceeded that reported from field studies. The microcosm system could be used for maintaining seedlings for use in the restoration of disturbed Thalassia beds.     

Factors Influencing Survival of Legionella pneumophila Serotype 1 in Hot Spring Water and Tap Water

The factors involved in the survival of Legionella pneumophila in the microcosms of both hot spring water and tap water were studied by examining cultivability and metabolic activity. L. pneumophila could survive by maintaining metabolic activity but was noncultivable in all microcosms at 42°C, except for one microcosm with a pH of <2.0. Lower temperatures supported survival without loss of cultivability. The cultivability declined with increasing temperature, although metabolic activity was observed at temperatures of up to 45°C. The optimal range of pH for survival was between 6.0 and 8. The metabolic activity could be maintained for long periods even in microcosms with high concentrations of salt. The cultivability of organisms in the post-exponential phase in a tap water microcosm with a low inoculum size was more rapidly reduced than that of organisms in the exponential phase. In contrast, the loss of cultivability in microcosms of a high inoculum size was significant in the exponential phase. Random(ly) amplified polymorphic DNA analysis of microcosms where cultivability was lost but metabolic activity was retained showed no change compared to cells grown freshly, although an effect on the amplified DNA band pattern by production of stress proteins was expected. Resuscitation by the addition of Acanthamoeba castellanii to the microcosm in which cultivability was completely lost but metabolic activity was maintained was observed only in part of the cell population. Our results suggest that L. pneumophila cell populations can potentially survive as free organisms for long periods by maintaining metabolic activity but temporarily losing cultivability under strict environments and requiring resuscitation by ingestion by amoebas.     

Cattle water troughs as reservoirs of Escherichia coli O157.

Environmental survival of Escherichia coli O157 may play an important role in the persistence and dissemination of this organism on farms. The survival of culturable and infectious E. coli O157 was studied using microcosms simulating cattle water troughs. Culturable E. coli O157 survived for at least 245 days in the microcosm sediments. Furthermore, E. coli O157 strains surviving more than 6 months in contaminated microcosms were infectious to a group of 10-week-old calves. Fecal excretion of E. coli O157 by these calves persisted for 87 days after challenge. Water trough sediments contaminated with feces from cattle excreting E. coli O157 may serve as a long-term reservoir of this organism on farms and a source of infection for cattle.     

Physiological characterization of viable-but-nonculturable Campylobacter jejuni cells

Campylobacter jejuni is a pathogenic, microaerophilic, gram-negative, mesophilic bacterium. Three strains isolated from humans with enteric campylobacteriosis were able to survive at high population levels (10(7) cells ml-1) as viable-but-nonculturable (VBNC) forms in microcosm water. The VBNC forms of the three C. jejuni strains were enumerated and characterized by using 5-cyano-2,3-ditolyl tetrazolium chloride-4',6-diamino-2-phenylindole staining. Cellular volume, adenylate energy charge, internal pH, intracellular potassium concentration, and membrane potential values were determined in stationary-phase cell suspensions after 48 h of culture on Columbia agar and after 1 to 30 days of incubation in microcosm water and compared. A notable increase in cell volume was observed with the VBNC state; the average cell volumes were 1.73 microliter mg of protein-1 for the culturable form and 10.96 microliter mg of protein-1 after 30 days of incubation in microcosm water. Both the internal potassium content and the membrane potential were significantly lower in the VBNC state than in the culturable state. Culturable cells were able to maintain a difference of 0.6 to 0.9 pH unit between the internal and external pH values; with VBNC cells this difference decreased progressively with time of incubation in microcosm water. Measurements of the cellular adenylate nucleotide concentrations revealed that the cells had a low adenylate energy charge (0.66 to 0.26) after 1 day of incubation in microcosm water, and AMP was the only nucleotide detected in the three strains after 30 days of incubation in microcosm water.     

Ways of determination of the intensity of the epidemic process in Shigella sonnei dysentery]

Proper view on the true prevalence of Sonne dysentery characterised by polymorphous clinical picture in which many cases coursed in subclinical form could be reached only by using additional active methods for detecting the infection rate of the population. For this purpose the authors applied passive hemagglutination test which permitted to reveal the response of the organism to the antigenic stimulation in the course of two months after the sustained sickness. Over 12 000 persons were examined. According to the results of passive hemagglutination test seasonal activization of the epidemic process occurred one month earlier than it was revealed by recording of the incidence of the disease. The results of the mentioned test also showed infection rate of the population with Sonne dysentery to be as a rule greater than established by the official statistics.     

Monitoring Arthrobacter protophormiae RKJ100 in a ‘tag and chase’ method during p-nitrophenol bio-remediation in soil microcosms

Monitoring of micro-organisms released deliberately into the environment is essential to assess their movement during the bio-remediation process. During the last few years, DNA-based genetic methods have emerged as the preferred method for such monitoring; however, their use is restricted in cases where organisms used for bio-remediation are not well characterized or where the public domain databases do not provide sufficient information regarding their sequence. For monitoring of such micro-organisms, alternate approaches have to be undertaken. In this study, we have specifically monitored a p-nitrophenol (PNP)-degrading organism, Arthrobacter protophormiae RKJ100, using molecular methods during PNP degradation in soil microcosm. Cells were tagged with a transposon-based foreign DNA sequence prior to their introduction into PNP-contaminated microcosms. Later, this artificially introduced DNA sequence was PCR-amplified to distinguish the bio-augmented organism from the indigenous microflora during PNP bio-remediation.     

植物种群生态学中的构件理论

植物种群生态学中的构件理论黎云祥,刘玉成,钟章成（四川师范学院生物系,南充６３７００２）（西南师范大学生物系,重庆６３０７１５）ＭｏｄｕｌａｒＴｈｅｏｒｙｉｎＰｌａｎｔＰｏｐｕｌａｔｉｏｎＥｃｏｌｏｇｙ．￥ＬｉＹｕｎｘｉａｎｇ;ＬｉｕＹｕｃｈｅｎｇ（...