One good example of adaptation is the camel and its ability to survive for long periods of time in the desert with very little water. Acclimation is a form of adaptation that an organism undergoes when transferred to a different habitat. Adjustment is made by modifying physical reactions to environmental changes, like shivering when exposed to cold weather.
Transformations that occur in adaptation tend to be permanent until new changes are needed again. These remaining members have adapted accordingly. Acclimation, on the other hand, is temporary adaptation to gradual changes in the natural habitat. A good example of this behavior is when a fresh water fish is caught and placed in an aquarium. The location may change but since sea water is not used, the new habitat pretty much mimics the old one, although it may experience a slight change in temperature and the space to swim around.
Eventually the fish learns to adapt by acclimation to its new surroundings. Adaptation is a natural process that occurs for every type of organism. This is to ensure continuity and survival of species. Acclimation may or may not occur in a habitat and if it does, it only takes a short time until an adjustment is made by animals and plants.
Ultimately, both terms deal with how living things cope with changes in their environment. Adaptation is a change in both physical and chemical composition of an organism brought about by habitat changes, while acclimation is a physical reaction made in order to adjust to said changes.
Adaptation is permanent, while acclimation is temporary. S1 , Supplementary Material online. This is the only mutation seen within the locus, highlighting the likelihood that highly specific changes to the expression of gcvT are adaptive under LTSP. The promoter region of the alcohol dehydrogenase gene adhP also contains a specific mutation across all five populations supplementary fig.
S1 B , Supplementary Material online. In the majority of cases one of two mutations occur within this locus supplementary fig. S1 D , Supplementary Material online. The second of these mutations appears in three of the five populations and falls within a known binding site of the small RNA GcvB, which regulates the expression of cycA at the posttranscriptional level Santos-Zavaleta et al. Specific high frequency convergent mutations are also observed within the genes dppA supplementary fig.
S1 C , Supplementary Material online and sstT supplementary fig. S1 E , Supplementary Material online. As with RNAPC, the fact that we observe very specific sites to be mutated in a convergent manner across populations indicates that it is specific changes to the expression or function of these five genes that are adaptive under LTSP.
In total, we observed 23 specific convergent mutations, each present across three or more of the five independently evolving LTSP populations supplementary table S6 , Supplementary Material online. For five additional genes, we found that across populations deactivating mutations inserting stops codons or frameshifts tended to occur A single example is presented in fig.
S2 , Supplementary Material online. These genes were the RNA chaperone gene proQ fig. The convergent occurrence of deactivating mutations within these genes suggests that it may be adaptive to remove the function of these specific genes under LTSP. Despite the high level of convergence with which adaptations occur between independently evolving LTSP populations, we find that adaptive alleles never fix across any entire individual population.
Instead multiple genotypes tend to compete for dominance across all populations and time points, in a pattern of soft sweeps fig. As a result, LTSP populations continuously maintain within them very high levels of genetic variation, even as they adapt in a highly convergent manner to prolonged resource exhaustion. The pattern of soft sweeps, which is observed when examining data from nonmutators, suggests that, even for them, adaptation continues to not be limited by mutational input, up to three years under resource exhaustion.
Further studies will be required in order to establish whether the maintenance of multiple genotypes over very long periods of time under LTSP is driven by balancing selection, clonal interference, or by other processes. Populations maintain high levels of genetic variation up to three years under LTSP.
A clear pattern of clonal interference by which several genotype compete for dominance across time points can be seen. Muller diagrams depicting the relative frequencies of different haplotypes segregating within LTSP populations 1, 3, and 5 are presented. The x -axis indicates the sampling times not to scale.
In population 3, which included mutator clones once the mutator lineage emerged, we do not depict the variation occurring within it, as it is too extensive to draw accurately. This lineage is represented in blue in the population 3. Due to very high frequencies of mutator clones within populations 2 and 4, we do not present Muller plots for these populations.
Muller plots were produced using the R package MullerPlot Farahpour et al. Combined, we observe both mutation accumulation with time and fluctuations in the frequencies of genotypes, as cell numbers remain stable over long periods of time.
This strongly suggests that cellular replication continues under LTSP, up to three years into these experiments. As already mentioned, we observed within three of the five LTSP populations the emergence of mutator clones, which acquired a mutation within a mismatch repair gene supplementary table S2 , Supplementary Material online. In populations 2 and 3, mutator clones carried mutations within the mutS gene. In population 4, a majority of mutators carried a mutation within mutL , whereas a minority carried a mutation within the gene mutH.
Interestingly, the three populations in which mutator clones were observed by day 64 of our experiments, continued to include such clones, at observable frequencies, up to three years into the experiment fig.
In contrast, in the two populations in which such clones were not observed by day 64, no such clones were observed up to three years into our experiments. Five populations are not, in our opinion, sufficient to be certain that this pattern by which mutators emerge under LTSP early or not at all is a general trend.
However, in the future, it might be interesting to examine whether this is indeed a general trend through the establishment of additional LTSP populations. Dynamics of mutator evolution under LTSP. A — C Clones that vary in their mutation rates coexist for long periods of time under resource exhaustion in all LTSP populations in which mutators evolved.
For each population, the relative frequency of each type of clone present within that population is depicted. In population 4, mutL clones sampled from days and 1, are marked using a different color from mutL clones extracted at earlier time points, due to their larger than expected mutation accumulation. It is, however, important to note that we did not observe a significantly higher frequency of development of rif resistance within mutL clones extracted during or after day and mutL clones extracted prior to day D Enhanced mutation rate mutators emerge within population 2.
Numbers of mutations accumulated by individual population 2 clones, as a function of time spent under LTSP. Nonmutator clones are represented by black triangles. Mutator clones are represented by magenta dots. Both axes are presented on a logarithmic scale. E Higher fractions of mutations fall within convergently mutated genes in clones with lower mutation rates. For each type of clone, the number of mutations falling within genes mutated in 1, 2, 3, 4, or all 5 populations is presented.
F Higher transition bias of synonymous mutations, counted only once, within mutators compared with nonmutators.
G Higher transition bias of nonsynonymous substitutions occurring within convergently mutated genes, within mutators compared with nonmutators. For F and G , numbers below each pie chart indicate the total numbers of mutations used to calculate the percentages presented in that pie chart. In population 3, mutators and nonmutator clones coexist at high frequencies up to 3 years under LTSP fig.
In populations 2 and 4, mutator clones rose to very high frequencies, leading to us sequencing only such clones at day 1, of the experiment. However, we did observe, out of the approximately ten clones sequenced, one nonmutator clone in each of these populations at day fig. We can therefore conclude that mutator and nonmutator clones tend to coexist for long periods of time under LTSP. It is important to note that while we did not observe any nonmutator clones in populations 2 and 4 at day 1,, this does not mean that they are necessarily not present within the population.
After all, by sequencing approximately ten clones out of millions of cells present within each population, we can only hope to identify the most frequent genotypes. In population 2, mutator clones, carrying a MutS TK mutation were first observed at day Up till day 64 clones carrying the TK MutS mutations had a rather similar number of mutations to each other, which ranged on the order of twice as many mutations as clones that did not carry a mutator mutation supplementary table S3 , Supplementary Material online.
However, at day , mutators seemed to diverge into three clusters fig. All mutator clones, irrespective of their accumulated number of mutations, carried the same TK MutS mismatch repair mutation. Within population 2, enhanced mutators were also observed at the later time points of our experiments, but always coexisted with initial mutators fig. In order to attempt and identify more of the clones with the enhanced mutator phenotype and examine whether these contain a secondary mutation explaining their higher mutation rate, we sequenced five additional clones from population 2 day after plating clones on plates containing the antibiotics rifampicin rif or nalidixic acid.
By sequencing clones that developed antibiotic resistance we hoped to enrich for clones that acquired a larger number of mutations overall. Indeed, all five antibiotic-resistant clones sequenced carried the MutS TK mutator mutation, and each acquired a total of 52, 59, , , and mutations, placing them in the enhanced mutator category. All 16 enhanced mutator clones identified throughout the experiment contained a mutation within the gene dnaQ.
In contrast, none of the 60 initial mutator clones carry such a mutation. It was previously shown that mutations within dnaQ can greatly increase mutation rates Echols et al. Intriguingly, the three day clones that accumulated between 52 and 79 mutations carried a GD DnaQ mutation, whereas the five that accumulated over mutations by day suffered a different mutation within DnaQ EK.
At later time points only the EK mutation was observed, fitting with the higher mutation accumulation rates of all enhanced mutator clones sequenced from day onward fig. Next, we wanted to independently verify that the different types of mutators identified in population 2 indeed differ in their mutation rates, as expected from their patterns of mutation accumulation.
To do so, the frequencies with which the four types of clones segregating within population 2 develop resistance to the antibiotic rif, following overnight growth in fresh LB without rif, was compared supplementary fig.
S3 , Supplementary Material online. As expected, nonmutator clones developed resistance at the lowest average frequency 3. The GD DnaQ enhanced mutators developed resistance at an average frequency higher than that of the initial mutators 4. Thus, it appears that fitting with rates of mutation accumulation under LTSP, the three mutator types evolving within population 2 indeed vary in their mutation rates, with initial mutators, which were the first to emerge having the lowest mutation rates and the EK DnaQ enhanced mutators having the highest.
Although mutators and nonmutators coexist within population 3 throughout the examined time points, at the final time point, the two sequenced mutators seemed to have acquired fewer mutations than we would expect from previous trends supplementary fig.
S4 , Supplementary Material online. These results were somewhat suspect given the fact that the two sequenced mutator clones had relatively low-sequencing coverage supplementary table S1 , Supplementary Material online. To further examine this, we examined the rates with which nonmutator and mutator population 3 clones extracted from the final time point day 1, , and from the previous time point day develop resistance to the antibiotic rif, following overnight growth in fresh LB without rif supplementary fig.
We found that mutator clones extracted at both time points had a similar rate of rif resistance that was significantly higher than the rate observed for the nonmutators. Our results thus suggest that mutators and nonmutators coexist within population 3, up to at least three years under LTSP.
Different types of mutators coexist over time within population 4. However, in this population, the differences in mutation rates between the mutator types seem to be less extensive. In population 4, we first observed mutators carrying a mutation within the mismatch repair gene mutL at day At day , we observed the mutL mutators alongside a second type of mutators carrying a mutation within mutH.
At day , both mutL mutators and mutH mutators carried a rather similar number of mutations supplementary fig. S5 , Supplementary Material online , which was consistent with the number of mutations observed for the initial mutators within populations 2 and 3 at day supplementary fig.
S6 , Supplementary Material online. At day we observed only the mutL mutators and these again carried a number of mutations which was consistent with that observed within initial mutators within populations 2 and 3 supplementary figs. S5 and S6 , Supplementary Material online. However, at day , we again observed both mutL and mutH mutators. While the mutH mutators seemed to accumulate mutations at a rate consistent with initial mutators, the mutL mutators acquired more than three times as many mutations, indicating that they may have increased their mutation rate further supplementary fig.
At day 1,, only the putative enhanced mutator mutL clones were observed. To further compare the mutation rates of the different types of mutators found within population 4, we characterized the frequency with which four types of population 4 clones develop resistance to the antibiotic rif following overnight growth in the absence of that antibiotic supplementary fig.
We found that a nonmutator clone extracted from population 4 at day developed resistance to rif at an average frequency of 5. The mutH clone extracted from the same population and time point developed resistance to rif at significantly higher frequencies 2. Although the mutH clone used for this analysis accumulated 31 mutations by day , the mutL clone we used, which was extracted from the same time point, accumulated mutations. Fitting with this, the mutL clone developed rif resistance following overnight growth at significantly higher frequencies, compared with the mutH mutator clone 3.
Based on the relative jump in the numbers of mutations accumulated by the mutL mutator clones, between days and , we expected that the mutL clones may have developed a higher mutation rate during that time.
We find that ratios of the rates of nonsynonymous to synonymous substitutions accumulated by nonmutators, initial mutators, and population 4 putative-enhanced mutators are all significantly higher than one table 2. This indicates that within these three clone types mutation accumulation tends to be dominated by positive selection. Further supporting this is the high fraction of mutations accumulated within such clones that fall within genes that are mutated across multiple populations fig.
Positive selection appears to be affecting mutation accumulation more strongly within nonmutators than within initial mutators. In sharp contrast, the vast majority of mutations found within population 2 enhanced mutator clones occur within genes that are not mutated in any of the other populations fig.
This constitutes a signal of purifying selection dominating patterns of mutation accumulation Graur and Wen-Hsiung In other words, population 2 enhanced mutators acquire a substantial number of deleterious mutations due to their extremely high mutation rates.
The extremely high mutation rate of the population 2 enhanced mutators therefore seems to impose on them a high deleterious burden. Yet, despite this deleterious burden, they persist alongside nonmutators at least up till day and alongside initial mutators at least up to day 1, , within population 2 fig. What advantage could population 2 enhanced mutator clones carry that enables them to persist alongside lower mutation rate clones, despite their deleterious burden?
One possibility is that the higher mutation rate of these clones may enable them to accumulate higher numbers of adaptive mutations, counterbalancing the deleterious effects of mutation accumulation. As described above, we identified 98 loci that are mutated in a convergent manner across three or more of the five LTSP populations. The mutations observed within our clones that fall within these loci are likely to be adaptive under LTSP. By day 1, of our experiments, non-mutator and initial mutators accumulated mutations within At the same time, the population 2 enhanced mutator clones accumulated mutations within Thus it appears that while the higher mutation rates of the population 2 enhanced mutators led to a higher accumulation of deleterious mutations, it also enabled these clones to acquire a higher number of adaptive mutations.
A previous study by Gentile et al. However, to our knowledge, we are the first to demonstrate such an event arising spontaneously within the context of an evolutionary experiment. Indeed, the opposite trend is often expected by which following the emergence of a mutator, antimutator alleles will tend to shift rates of mutation back down Couce and Tenaillon Indeed, in the LTEE the greatest fitness gains occurred early on, with a later pattern of diminishing returns Lenski and Travisano The fact that in our experiment, we see mutators with higher mutation rates coexisting at high frequencies alongside those with lower mutation rates may be the result of adaptive mutation availability remaining high up to three years under LTSP.
One possibility for why adaptive mutations may continue to be available under LTSP is that conditions might be changing, requiring cells to continuously adapt to these changes. A second possibility is that conditions remain fairly constant, but that the ancestral E. More research will be needed in order to distinguish between these two possibilities. In addition to affecting mutation rates, mutator mutations also have the potential to affect mutational spectra i. In order to estimate mutational spectra, it is necessary to examine mutations accumulated in the absence of selection Hershberg and Petrov However, mutations accumulated under LTSP are strongly affected by selection.
We therefore attempted to examine mutational spectra by focusing on synonymous mutations, which are less likely to be subject to strong selection and by considering each synonymous mutation only once, irrespective of the number of clones it appeared in. This observed enrichment in transition mutations within mutators was previously demonstrated for a mutL mutator in a mutation accumulation study Lee et al. Such an increased transition bias may be expected to occur within mutators that are defective in their mismatch repair genes.
Due to the structure of the genetic code, transitions are less likely than transversions to lead to nonsynonymous substitutions. All the laboratory procedures were carried out in a low light environment.
The values were expressed in nmol. Chlorophyll a fluorescence parameters: Chlorophyll a fluorescence parameters were determined between a. The following chlorophyll a fluorescence emission parameters were recorded: F 0 minimal fluorescence , F m maximum fluorescence and nonphotochemical quenching coefficients qN and NPQ. The values are presented as the mean of ten measurements, representing ten replicates. Metal analysis in plants: According to Table 2 , the roots young and old were the main sites of metal accumulation when compared to the shoots petioles and leaf limb for all metals.
Manganese and Fe were the metals detected in highest concentrations for all tissues. Only Cr was not detected in shoots, and in addition to Pb and Ni these were the metals found in the lowest concentration. In most cases Fe, Cu, Cr, Pb and Ni , the samples taken in the middle PSR contained the higher metals concentrations than another collecting points, although in some cases statistical difference was not observed between samples from middle and upper PSR Table 2.
Photosynthetic pigments: The photosynthetic pigments chlorophyll a , b and carotenoids were the highest in plants from the middle and upper PSR Table 3. Chlorophyll a fluorescence parameters: The chlorophyll a fluorescence ratios emphasizes the similarities of responses between plants from middle and upper PSR and between plants from lower PSR and IR Figure 2.
Correlation between qN and carotenoids had r : 0. Iron and Mn were the elements detected in the highest concentrations Table 2 , predominantly in roots. According to Ajmal et al. However, Fe and Mn values detected in our study are much higher than those reported by Ajmal et al. Higher concentrations of Fe detected in plants from PSR are probably due to the natural characteristics of this basin Carvalho et al. Other studies on water hyacinth have also shown this Soltan and Rashed ; Lu et al.
The presence of metals in tissues of the aerial part in higher concentrations than usually required by the plant metabolism may inhibit growth by interfering in important physiological processes, such in photosynthesis and respiration Yruela, However, it should be also considered that the apparent preferential sequestration of high concentration of Fe and Mn in the roots may be due to methodological limitations, like inefficient washings in distilled water to remove Fe and Mn adsorbed onto the root surface.
Vesk et al. The formation of Fe plaques on aquatic plants roots has been also reported Povidisa et al. When another hyperaccumulator Arabidopsis halleri was submitted to growth in a hydroponic solution containing Cd and Zn, the cell walls of epidermal cells retained practically all these ions, suggesting that accumulation of these metals may be due to the precipitation of Cd and Zn phosphate in the cell wall of root cells Cosio et al.
However, when metals enter in the cell, in general they are restrained in vacuole, in a process crucial of detoxification. The sequestration of these elements into the vacuole would drastically reduce their concentration in the cytoplasm, thus preventing or avoiding the damage to the physiological and biochemical cell processes Prasad, In the present study Cr was the only metal detected only in roots.
However, Cr was already found in shoots of water hyacinth Klumpp et al. According to Table 2 , the higher concentrations of Cr were observed in water hyacinth roots from the middle PSR, in some cases with values inferior to concentrations detected in plants from other polluted rivers Table 4.
In this study, other elements with lower concentrations than plants inhabiting other world rivers were Pb, Ni, Cu, and Zn. Thus, it is possible that the Zn and Cr concentrations of this study may not be considered detrimental to water hyacinth development. Hu et al. The middle and upper PSR are the collection points that are under the greatest human influence. These regions contain steel, metal foundry, chemical, paper, petrochemical industries and middle and large-sized cities.
These activities may be altering the natural conditions of the river due to the insertion of greater quantities of some metals in this ecosystem Malm et al. In middle PSR, Azevedo et al. Despite the confirmed presence of polluting metals in water hyacinth in this study, according to fluorescence a chlorophyll data these plants are not stressed. Adams and Demmig-Adams and Falbel et al. Bjoerkman and Demmig suggest a most narrow range 0. Our results varied from 0. The absence of necrosis, yellowing, blight or symptoms or any other morphological alteration not shown reinforces that suggestion.
This fact confirms previous data from Paiva et al. In these plants, as well as in plants from the upper PSR, a higher photosynthetic pigments content, including carotenoids, was observed Table 3. The positive correlation between these quenchings and the content of carotenoids suggests energy dispersion in these plants as a provable mechanism to reduce load on the electron transport chain.
The test of correlation between nonphotochemical quenchings qN e NPQ and the content of carotenoids suggests that other components, different than carotenoids, are implicated with energy dissipation absorbed in the form of heat. These factors may be associated with the carotenoids composition and the participation of a low molecular weight protein known as PsbS Li et al. PsbS protein is responsible for the linkage of the zeaxantine from the antenna complex, LHCII, with the reaction center from the PS II , making easy de-excitation of chlorophyll singlet excited with the emission of non-radiant energy, that is, in the form of heat Niyogi et al.
Carotenoids composition is linked to the xantophiles cycle conversion of violanthin to zeaxantine , responsible by heat dissipation in the process of protection of the PS II Adams and Demmig-Adams, The NPQ is associated with this conversion that consists of de-epoxidation of the epoxide groups from violaxanthin forming cyclohexenyl rings.
This mechanism lowers the energy of the carotenoid S1 state to approximately the same level as the chlorophyll a S1 state and induces a potential new pathway for reversible single-single energy transfer from chlorophyll a to zeaxanthin. Eullaffroy et al. However, little information is available in scientific literature about this adaptative mechanism in water hyacinth. The sparse data available are still conflicting, suggesting that this is not an obligate response or a short time response for this species under stress conditions.
Paiva et al.
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