Cadmium-mediated resistance to metals and antibiotics in a cyanobacterium

Summary Cadmium-resistant strains of the cyanobacterium Nostoc calcicola were isolated through the step-wise transfer of the organism to higher levels of the metal. One of the Cd-resistant strains (Cd^r–10) showed cross-resistance to antibiotics like neomycin (1 g/ml), chloramphenicol (3 g/ml) but not to streptomycin. The Cd-resistant strain also tolerated elevated levels of metals such as zinc (20 ppm) and mercury (1 ppm). The stability of the metal-resistance required the presence of Cd²⁺ ions in the growth medium. It is suggested that metal resistance may also be determined by gene(s) on the antibiotic resistance plasmids in cyanobacteria.     

Trade-offs and coexistence in microbial microcosms

Trade-offs among the abilities of organisms to respond to different environmental factors are often assumed to play a major role in the coexistence of species. There has been extensive theoretical study of the role of such trade-offs in ecological communities but it has proven difficult to study such trade-offs experimentally. Microorganisms are ideal model systems with which to experimentally study the causes and consequences of ecological trade-offs. In model communities of E. coli B and T-type bacteriophage, a trade-off in E. coli between resistance to bacteriophage and competitive ability is often observed. This trade-off can allow the coexistence of different ecological types of E. coli. The magnitude of this trade-off affects, in predictable ways, the structure, dynamics and response to environmental change of these communities. Genetic factors, environmental factors, and gene-by-environment interactions determine the magnitude of this trade-off. Environmental control of the magnitude of trade-offs represents one avenue by which environmental change can alter community properties such as invasability, stability and coexistence. This revised version was published online in August 2006 with corrections to the Cover Date.     

Adaptive radiation in microbial microcosms

It has often been argued that evolutionary diversification is the result of divergent natural selection for specialization on alternative resources. I provide a comprehensive review of experiments that examine the ecology and genetics of resource specialization and adaptive radiation in microbial microcosms. In these experiments, resource heterogeneity generates divergent selection for specialization on alternative resources. At a molecular level, the evolution of specialization is generally attributable to mutations that de-regulate the expression of existing biosynthetic and catabolic pathways. Trade-offs are associated with the evolution of resource specialization, but these trade-offs are often not the result of antagonistic pleiotropy. Replicate adaptive radiations result in the evolution of a similar assemblage of specialists, but the genetic basis of specialization differs in replicate radiations. The implications of microbial selection experiments for evolutionary theory are discussed and future directions of research are proposed.     

Macro-zooplankter responses to simulated climate warming in experimental freshwater microcosms

1. We report data collected from 48 replicated microcosm communities created to mimic plant‐dominated shallow lake and pond environments. Over a 2‐year period, the microcosms were subjected to warming treatments (continuous 3 °C above ambient and 3 °C above ambient during summer only), a nutrient addition treatment and the presence or absence of fish. We tracked macro‐zooplankter dynamics, censusing cladoceran populations at the species level, copepods at the order level and ostracods as a class. 2. Responses to warming were subtle. Cladoceran diversity and overall abundance were not significantly affected by warming, although measures of community evenness increased. Warming effects on patterns of population trajectories tended to be strongly seasonal and most apparent during periods of pronounced increase. Populations of the prevalent cladocerans, Chydorus sphaericus and Simocephalus vetulus, displayed idiosyncratic patterns, with evidence in the case of S. vetulus for a negative relationship between warming and body‐size at maturity. Copepod populations were reduced in size by warming, but those of ostracods increased. 3. The effects of the nutrient addition and fish treatments were strong and consistent, interacting little with warming effects in statistical models. Zooplankter abundance tended to be the highest in the fish‐free microcosms receiving additional nutrient inputs and lowest when fish were present and no nutrients were added. Both treatments reduced cladoceran diversity and community evenness. 4. We suggest that warming, independently, is unlikely to supplant the effects of changing nutrient loading and fish predation as the major driver of zooplankter dynamics in shallow lakes and ponds. Moreover, in the situations where warming was of significant influence in our experiment, the distinction between summer‐only warming and year‐around warming was blurred. This suggests that warming effects were most pervasive during the summer, at the upper end of the temperature spectrum.     

Monitoring genetically engineered microorganisms in freshwater microcosms

Summary The effectiveness of gene probe methods for tracking genetically engineered microorganisms (GEMs) in the environment was tested by inoculating nutrient-supplemented freshwater microcosms withAlcaligenes A5 (a naturally occurring 4-chlorobiphenyl degrader) orPseudomonas cepacia AC1100 (a genetically engineered 2, 4, 5 T-degrader) and following the fates of the introduced bacterial populations. Colony hybridization of the viable heterotrophic bacterial populations and dot blot hybridization of DNA recovered from the total microcosm microbial communities showed persistence of bothAlcaligenes A5 andP. cepacia AC1100 in the microcosms in the presence and absence of the xenobiotic substrates that these organisms biodegrade. Although there was a gradual decline in the added populations, both of the bacterial populatins were still detected in the microcosms two months after their introduction into the microcosms. Addition of 2, 4, 5-T enhanced the survival ofP. cepacia AC1100 — and 4-chlorobiphenyl addition resulted in increased levels ofAlcaligenes A5. The results indicate that both organisms may persist for very long periods in freshwater habitats.     

The role of thiamine inYersinia kristensenii resistance to antibiotics and heavy metals

The resistance to divalent metal ions, antibiotics and H₂O₂ was investigated inYersinia kristensenii strains 13, 15, 18 by performing subcultivations with CdSO₄ (20 and 100mg/L) in nutrient agar (NA) and M9 medium with thiamine. Metal resistance of all three strains in NA was the same and decreased in the following sequence: Ni>Zn=Co>Cd. The chloramphenicol (Cmp) resistance ranged between 32 and 256 mg/L and the H₂O₂ sensitivity was very low or even zero. In the presence of thiamine the metal resistance sequence changed to Zn=Cd>Ni, Co, Ni and Co tolerance being 10–20 mg/L. Cmp resistance of all strains increased to 256 mg/L and H₂O₂ sensitivity also rose. In Cd-treated cultures, the ratio of glucose to thiamine in culture medium affected Cd resistance. At normal content of glucose and thiamine (5 g/L and 5mg/L), Cd resistance markedly decreased coincident with thiamine exhaustion in these slowly-growing cultures. The Cmp resistance decreased to 16 mg/L, Ni and Co intolerance and H₂O₂ hypersensitivity appeared. At lowered glucose or thiamine levels (5 g/L and 2.5 mg/L or 2.5 g/L and 5 mg/L) a marginal decrease of Cd resistance took place in response to limited glucose uptake. Low thiamine or low-glucose cultures were resistant to H₂O₂, and exhibited a small decrease in Cmp resistance and a low Ni, Co tolerance. The adaptation of strain 15 to Cd induced only a small decrease of Cd resistance. Lowered glucose-to-thiamine ratio in culture medium probably induced in Cd-treated cultures a response triggering Cd resistance.     

Temporal dynamics of microbial communities in microcosms in response to pollutants

Elucidating the mechanisms underlying microbial succession is a major goal of microbial ecology research. Given the increasing human pressure on the environment and natural resources, responses to the repeated introduction of organic and inorganic pollutants are of particular interest. To investigate the temporal dynamics of microbial communities in response to pollutants, we analysed the microbial community structure in batch microcosms that were inoculated with soil bacteria following exposure to individual or combined pollutants (phenanthrene, n‐octadecane, phenanthrene + n‐octadecane and phenanthrene + n‐octadecane + CdCl₂). Subculturing was performed at 10‐day intervals, followed by high‐throughput sequencing of 16S rRNA genes. The dynamics of microbial communities in response to different pollutants alone and in combination displayed similar patterns during enrichment. Specifically, the repression and induction of microbial taxa were dominant, and the fluctuation was not significant. The rate of appearance for new taxa and the temporal turnover within microbial communities were higher than the rates reported in other studies of microbial communities in air, water and soil samples. In addition, conditionally rare taxa that were specific to the treatments exhibited higher betweenness centrality values in the co‐occurrence network, indicating a strong influence on other interactions in the community. These results suggest that the repeated introduction of pollutants could accelerate microbial succession in microcosms, resulting in the rapid re‐equilibration of microbial communities.     

Resources drive trade‐off between viral lifestyles in the plankton: evidence from freshwater microbial microcosms

Viruses have evolved different life strategies for coping with environmental challenges and this is a key explanation for their omnipresence in aquatic systems. However, factors that determine the balance between lytic versus lysogenic decision within natural virioplankton are poorly documented, primarily in freshwaters. This study was designed to investigate the experimental short‐term (24 h incubation) effects of added organic and inorganic nutrients on the two viral lifestyles in nutrient‐depleted freshwater microbial (i.e. < 0.8 μm fraction) microcosms, using mitomycin C as prophage inductor agent. In the absence of mitomycin, viral lytic production increased as a functional response to the strong stimulation of bacterial growth rates (0.7–0.8 day^?1) by the added nutrients, primarily the organic nutrients which appeared scarcer than inorganic nutrients and was related to the sampling period and the geomorphological peculiarities of Lake Pavin. In the presence of mitomycin, temperate phage production (frequency of lysogenically infected bacterial cells, FLC = 17–19% of total cells) significantly exceeded lytic production (frequency of lytically infected bacterial cells, FIC = 9–11%) in natural samples (i.e. without nutrient additions) as a result of enhanced prophage induction, which relatively increased with the decreasing contact probability between viruses and their potential hosts. In contrast, addition of nutrients drastically reduced FLC (< 4%) and increased FIC (> 22%). Both variables were antagonistically correlated as was the correlation between FLC and bacterial growth rates, supporting the idea that lysogeny may represent a maintenance strategy for viruses in harsh nutrient/host conditions which appeared as major instigators of the trade‐off between the two viral lifestyles. Overall, at the community level, we reject the hypothesis that nutrients but mitomicyn C stimulate temperate phage induction, and retained the hypotheses that nutrients rather (i) stimulate lytic viruses via enhanced host growth and (ii) when limiting, promote lysogenic conversion in natural waters.     

Fluctuating resource availability increases invasibility in microbial microcosms

The fluctuating resource hypothesis (FRH) proposes that fluctuations in resource supply can temporally reduce competitive pressure from resident species, thereby providing ephemeral opportunities for invading species. Although FRH has the potential to integrate many existing hypotheses regarding mechanisms of community invasibility, previous tests and evaluations of FRH were based on single trophic level, did not take the timing effect into account, and had difficulties in distinguishing the effects of resource pulses from other simultaneous processes. Here we test FRH in multi‐trophic aquatic microcosms by creating resource pulses, by controlling resource quantity, propagule supply and pulse recurrence frequency, and by manipulating the timing of pulses relative to the timing of the arrival of new species (i.e. invaders) to local communities. The novelty of our work lies in that we directly manipulate resource pulse timing relative to invader introduction events and thus demonstrate the importance of this timing effect for community invasibility. Our study supports FRH in general: invasion success was positively related to resource pulses, and invaders had strong performance in treatments receiving coincident pulses, although not all invaders gained more benefit when resources were supplied at large‐magnitude than supplied at continuous rates. Since many ecosystems worldwide are experiencing high rates of anthropogenic nutrient input and increasing rates of precipitation, these ecosystems are potentially more fragile and susceptible to invasion. More experiments across multiple ecosystem types are needed to help formulate a general theory of community invasibility.     

Interactions between algae and the microbial loop in experimental microcosms

We conducted a short-term microcosm experiment to study the direct and indirect effects of a bacterivore on bacteria and the dynamics of two species of green algae. We introduced Scenedesmus , Chlorella and Colpidium , a bacterivorous ciliate, successively in a carbon-rich medium. Bacteria were introduced with Scenedesmus , Chlorella and Colpidium . The experiment lasted 40 days, preventing us from detecting whether the populations had reached equilibrium. The bacterivore had a positive effect on both species of algae by limiting the abundance of bacteria. In absence of the bacterivore, bacteria did not exclude the two algal species, despite the high carbon:nutrient ratio of the medium. Unexpectedly, by the end of the experiment the bacterivore declined in all microcosms. Also, Chlorella growth was impeded by the presence of Scenedesmus . These two observations might be explained by allelopathic interactions. Our experiment suggests that the functioning of such a simple community is far more complex than assumed in previous theoretical and experimental models. Studying the dynamics of the system, however, allowed us to disentangle species interactions.     

Survival and persistence of human and ruminant-specific faecal Bacteroidales in freshwater microcosms

Amplification of host-specific markers from Bacteroidales faecal anaerobes can rapidly identify the source of faecal pollution. It is necessary to understand persistence and survival of these markers and marker cells, both to interpret quantitative source-tracking data, and to use such data to predict pathogen occurrence. We measured marker persistence and cell survival of two human (HF134, HF183) and two ruminant (CF128, CF193) faecal Bacteroidales markers, compared with Escherichia coli and enterococci. Freshwater microcosms were inoculated with fresh cattle or human faeces and incubated at 13°C in natural light or darkness. Marker persistence was measured by polymerase chain reaction (PCR) and quantitative PCR. Survival of marker cells was measured by real-time quantitative PCR. There was no difference in persistence between the two human-specific Bacteroidales DNA markers in the light and dark microcosms. Cell survival profiles of the two human markers were also similar; both were significantly affected by light. Ruminant markers persisted and survived longer than human markers (14 versus 6 days respectively). CF193 decreased more rapidly than CF128, and light significantly affected CF128 but not CF193. These results support use of host-specific faecal Bacteroidales markers as indicators of recent faecal pollution, but suggest that caution is needed in interpreting quantitative results to indicate proportional contribution of different sources, as individual markers differ in their survival, persistence and response to environmental variables. The survival and persistence profiles for Bacteroidales markers are consistent with survival profiles for several faecal pathogens.     

Beta-lactamases and bacterial resistance to antibiotics

The efficiency of β-lactam antibiotics, which are among our most useful chemotherapeutic weapons, is continuously challenged by the emergence of resistant bacterial strains. This is most often due to the production of β-lactamases by the resistant cells. These enzymes inactivate the antibiotics by hydrolysing the β-lactam amide bond. The elucidation of the structures of some β-lactamases by X-ray crystallography has provided precious insights into their catalytic mechanisms and revealed unsuspected similarities with the DD-transpeptidases, the bacterial enzymes which constitute the lethal targets of β-lactams. Despite numerous kinetic, structural and site-directed mutagenesis studies, we have not completely succeeded in explaining the diversity of the specificity profiles of β-lactamases and their surprising catalytic power. The solutions to these problems represent the cornerstones on which better antibiotics can be designed, hopefully on a rational basis.     

Temporal variation of magnetotactic bacterial communities in two freshwater sediment microcosms

Magnetotactic bacteria (MTB), which can mineralize nanosized magnetite or greigite crystals within cells, play important roles in biogeochemical processes, for example iron and sulfur cycling, and depositional remanent magnetization acquisitions. Despite decades of research, the knowledge of MTB distribution and ecology is still limited. In the present study, we investigated the temporal variation of MTB communities in freshwater sediment microcosms based on 16S rRNA genes and unifrac analyses. Two microcosms (MY8 and MY11) collected from two separate sites in Lake Miyun (Beijing, China) were analyzed. The majority of retrieved sequences belonged to alphaproteobacterial magnetotactic cocci in both microcosms (representing 64.29% of clones from MY8 and 100% of clones from MY11), whereas so-called ' Magnetobacterium bavaricum '-like MTB affiliated within Nitrospira phylum were exclusively found in microcosm MY8. Over a 3-month period, the temporal variation of MTB communities was evident in both microcosms. In addition, the phylogenetic discrepancy of MTB communities between two microcosms is more prominent than that of the same microcosm at different times, implying adaptation of MTB phylogenetic lineages to specific microenvironments. Among the physical–chemical parameters measured, a strong correlation was shown between nitrate and the main genetic variability of MTB communities, indicating that nitrate may influence the occurrence of MTB phylogenetic lineages in natural environments.     

Comparative analysis of growth and physio-biochemical responses of Hydrilla verticillata to different sediments in freshwater microcosms

The long-term effect of Hydrilla verticillata to different dredged sediments was investigated in laboratory aquatic microcosms. Two kinds of lake sediments, i.e., fertile sludge and brown clay, which were acquired by deep or slight dredging and differed in their nutrients levels and particle sizes, were used as growth substrate. One year after H. verticillata seedlings were transplanted into the microcosms, growth and physio-biochemical characters of the plants were estimated. In our study, sludge sediment eventually promoted the increase of the biomass, shoot length, bifurcation, nitrogen, phosphorus, soluble protein content of H. verticillata, but not root number and root mass ratio. Additionally, the soluble sugar content was significantly lower in summer (August) in the sludge sediment. Sediment nutrients also increased photosynthetic pigment content, while POD and SOD activities were not affected. The fertile sludge and brown clay formed by different dredging are quite different, but both sediments could meet the requirement of H. verticillata during early growth stage. The fertile sediment after moderate dredge-up fit the growth of H. verticillata. The brown clay formed after excessive dredging showed a lack of nutrients and therefore led to the weak growth of the aquatic plants. It is concluded that moderate dredging was suitable for H. verticillata growth and for absorbing nitrogen and phosphorus from eutrophic fresh water. The experiment also suggested that submersed aquatic plant restoration in freshwater can be promoted by human assistance.     

Distinctive patterns in prokaryotic community composition in response to viral lysis and flagellate grazing in freshwater microcosms

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