Differentiation in sex investment by clones and populations of Daphnia

Dormancy is an ecological strategy by which organisms avoid stressful environments, but it also can have genetic consequences. Many facultative parthenogens shift from asexual to sexual reproduction to enter dormancy. Hence, conditions that favour dormancy are predicted to select for more sex, which should increase clonal diversity. We examined lake populations of Daphnia that face different ecological risks to remaining active year‐round, and quantified the extent to which they have differentiated in their investment in dormancy and sex. There was substantial genetic variation among populations and clones for sex induction and production of dormant eggs, and striking evidence of gender specialization. We also observed a positive association between the magnitudes of population‐level investment in dormancy and of variance among clones in sex induction. These results document an ecological gradient in dormancy that is manifest as a genetic gradient in clonal variation for the propensity to engage in sex.     

Polyandry by wood mice in natural populations

The microhabitat used by the garden dormouse Eliomys quercinus during its nocturnal activity was examined. Twenty-three variables describing habitat structure were measured at 100 trapping points. Logistic regression models were utilized to select the variables that discriminate between used and avoided trapping points and, in a series of pairwise contrasts, between trap sites used by different sexes, age classes and animals in different reproductive periods. Used sites were characterized by a higher (>40%) rock cover, a thicker shrub layer and a younger understory with trees of smaller trunk diameter. These variables describe areas with rockfalls from the upper slope, where trees were younger and smaller, the canopy closure reduced and the shrub layer more developed than in other parts of the forest. Dense shrubby vegetation provided protection from aerial predators and, in conjunction with rocks and stones, might have made hunting by birds and mammals more difficult. Garden dormice may also have been attracted by rocky areas acting as a heat source during the night. The selection of rocky areas was more important in the first months of the active period, when animals emerged from hibernation and started the mating season. At the end of summer, the animals used areas richer in herbs, where insects and other food resources were probably more abundant.     

Extinction of populations by random influences

A unifying approach described by a random birth and death process which includes both environmental and demographic noise is introduced. It is shown that both of these noise sources play an essential role in extinction processes in general. The probability distribution of the lifetime of a population is determined and its dependence on the parameters of the model is discussed. Finally a population divided into subpopulations is modeled. The lifetime of this ensemble of subpopulations is compared to the lifetime of one large population.     

Detection and counting of Nitrobacter populations in soil by PCR.

Although the biological conversion of nitrite to nitrate is a well-known process, studies of Nitrobacter populations are hindered by their physiological characteristics. This report describes a new method for detecting and counting Nitrobacter populations in situ with the PCR. Two primers from the 16S rRNA gene were used to generate a 397-bp fragment by amplification of Nitrobacter species DNA. No signal was detected from their phylogenetic neighbors or the common soil bacteria tested. Extraction and purification steps were optimized for minimal loss and maximal purity of soil DNA. The detection threshold and accuracy of the molecular method were determined from soil inoculated with 10, 10(2), or 10(3) Nitrobacter hamburgensis cells per g of soil. Counts were also done by the most-probable-number (MPN)-Griess and fluorescent antibody methods. PCR had a lower detection threshold (10(2) Nitrobacter cells per g of soil) than did the MPN-Griess or fluorescent antibody method. When PCR amplification was coupled with the MPN method, the counting rate reached 65 to 72% of inoculated Nitrobacter cells. Tested on nonsterile soil, this rapid procedure was proved efficient.     

Degradability of polychlorinated phenols by bacterial populations in soil

The biodegradabilities of polychlorinated phenols including 5 isomers of trichlorophenols, 3 isomers of tetrachlorophenols and pentachlorophenol, were tested with 170 samples of soil collected from various environments. After the samples were inoculated into a succinate-containing mineral medium and incubated, the cultures were acclimatized to phenol concentrations from 10 to 100 ppm. Twenty six samples (15%) were observed to degrade 2, 4, 6-trichlorophenol (246TrCP) and a mixed sample of soil degraded 2, 3, 4, 6-tetrachlorophenol, but no degradation was seen with other chlorophenols. All of the mixed cultures acclimatized to and degrading 246TrCP also degraded phenol. For the degradation of 246TrCP, the NO₃′ ion was preferred to the NH₄⁺ ion as a nitrogen source. At concentrations below 500 ppm, 246TrCP was degraded completely within 8 d and the chloride ion was detected in the culture broth at an amount corresponding to that of the chlorinated phenol, although cell growth was inhibited at a 246TrCP concentration of 1,000 ppm. No possible intermediate product of 246TrCP was detected in the cultures.     

Utilization of chlorobenzoates by microbial populations in sewage.

Microorganisms in sewage decomposed 3.4-dichlorobenzoate and m-, p-, and o-chlorobenzoates. As the substrate disappeared, populations capable of growing on these compounds proliferated. Neither 2,4-dichlorobenzoate nor 2,3,6-trichlorobenzoate was destroyed by the sewage microflora. The addition of glucose or benzoate and m-chlorobenzoate to the sewage did not promote degradation of 2,4-di- or 2,3,6-trichlorobenzoates. The populations responsible for the biodegradation of the chlorinated compounds were initially less than 100 cells/ml. During the metabolism of m-chlorobenzoate, 5-chlorosalicylate and 4-chlorocatechol were formed.     

Utilization of chlorobenzoates by microbial populations in sewage.

Microorganisms in sewage decomposed 3.4-dichlorobenzoate and m-, p-, and o-chlorobenzoates. As the substrate disappeared, populations capable of growing on these compounds proliferated. Neither 2,4-dichlorobenzoate nor 2,3,6-trichlorobenzoate was destroyed by the sewage microflora. The addition of glucose or benzoate and m-chlorobenzoate to the sewage did not promote degradation of 2,4-di- or 2,3,6-trichlorobenzoates. The populations responsible for the biodegradation of the chlorinated compounds were initially less than 100 cells/ml. During the metabolism of m-chlorobenzoate, 5-chlorosalicylate and 4-chlorocatechol were formed.     

Biodegradation of trichloroethylene and toluene by indigenous microbial populations in soil.

The biodegradation of trichloroethylene (TCE) and toluene, incubated separately and in combination, by indigenous microbial populations was measured in three unsaturated soils incubated under aerobic conditions. Sorption and desorption of TCE (0.1 to 10 micrograms ml-1) and toluene (1.0 to 20 micrograms ml-1) were measured in two soils and followed a reversible linear isotherm. At a concentration of 1 micrograms ml-1, TCE was not degraded in the absence of toluene in any of the soils. In combination, both 1 microgram of TCE ml-1 and 20 micrograms of toluene ml-1 were degraded simultaneously after a lag period of approximately 60 to 80 h, and the period of degradation lasted from 70 to 90 h. Usually 60 to 75% of the initial 1 microgram of TCE ml-1 was degraded, whereas 100% of the toluene disappeared. A second addition of 20 micrograms of toluene ml-1 to a flask with residual TCE resulted in another 10 to 20% removal of the chemical. Initial rates of degradation of toluene and TCE were similar at 32, 25, and 18 degrees C; however, the lag period increased with decreasing temperature. There was little difference in degradation of toluene and TCE at soil moisture contents of 16, 25, and 30%, whereas there was no detectable degradation at 5 and 2.5% moisture. The addition of phenol, but not benzoate, stimulated the degradation of TCE in Rindge and Yolo silt loam soils, methanol and ethylene slightly stimulated TCE degradation in Rindge soil, glucose had no effect in either soil, and dissolved organic carbon extracted from soil strongly sorbed TCE but did not affect its rate of biodegradation.     

Biodegradation of trichloroethylene and toluene by indigenous microbial populations in vadose sediments

The unsaturated subsurface (vadose zone) receives significant amounts of hazardous chemicals, yet little is known about its microbial communities and their capacity to biodegrade pollutants. Trichloroethylene (TCE) biodegradation occurs readily in surface soils; however, the process usually requires enzyme induction by aromatic compounds, methane, or other cosubstrates. The aerobic biodegradation of toluene and TCE by indigenous microbial populations was measured in samples collected from the vadose zone at unpolluted and gasoline-contaminated sites. Incubation at field moisture levels showed little activity on either TCE or toluene, so samples were tested in soil suspensions. No degradation occurred in samples suspended in water or phosphate buffer solution; however, both toluene and TCE were degraded in samples suspended in mineral salts medium. TCE degradation depended on toluene degradation, and little loss occurred under sterile conditions. Studies with specific nutrients showed that addition of ammonium sulfate was essential for degradation, and addition of other mineral nutrients further enhanced the rate. Additional studies with vadose sediments amended with nutrients showed similar trends to those observed in sediment suspensions. Initial rates of biodegradation in suspensions were faster in uncontaminated samples than in gasolinecontaminated samples, but the same percentages of chemicals were degraded. Biodegradation was slower and less extensive in shallower samples than deeper samples from the uncontaminated site. Two toluene-degrading organisms isolated from a gasoline-contaminated sample were identified as Corynebacterium variabilis SVB74 and Acinetobacter radioresistens SVB65. Inoculation with 10⁶ cells of C. variabilis ml^–1 of soil solution did not enhance the rate of degradation above that of the indigenous population. These results indicate that mineral nutrients limited the rate of TCE and toluene degradation by indigenous populations and that no additional benefit was derived from inoculation with a toluene-degrading bacterial strain. Correspondence to: K.M. Scow     

Lower genetic diversity and hatchability in amphibian populations isolated by urbanization

Many amphibian populations worldwide have declined rapidly and been threatened with extinction in the past few decades because of human impacts on the environment. It is well known that urbanization reduces the genetic diversity of isolated populations. The concept that a reduction in genetic diversity leads to lower reproductive fitness has been predominantly supported by studies involving laboratory organisms, but has rarely been tested in wild populations. Here we examined whether genetic diversity affected hatchability, a population parameter related to reproductive success, in the populations of two pond-breeding amphibian species (Hynobius tokyoensis and Rana ornativentris) affected by urbanization. We surveyed 81 populations in the southwestern Kanto region of Japan. Mean hatchability of the populations was determined and genetic diversities were estimated via mitochondrial or microsatellite DNA analyses. Firstly, Random Forests (an ensemble machine learning method) models were applied to clarify the effects of environmental factors on both hatchability and genetic diversity. Subsequently, the relationships among environmental factors, genetic diversity, and mean hatchability were evaluated using path analysis. Mean hatchability was significantly affected by both urbanization and genetic diversity. This result shows that loss of genetic diversity may decrease a population’s reproductive success in the field.     

Genetic variability maintained by mutation and overdominant selection in finite populations

Mathematical properties of the overdominance model with mutation and random genetic drift are studied by using the method of stochastic differential equations (Itô and McKean 1974). It is shown that overdominant selection is very powerful in increasing the mean heterozygosity as compared with neutral mutations, and if 2Ns (N = effective population size; s = selective disadvantage for homozygotes) is larger than 10, a very low mutation rate is sufficient to explain the observed level of allozyme polymorphism. The distribution of heterozygosity for overdominant genes is considerably different from that of neutral mutations, and if the ratio of selection coefficient (s) to mutation rate (ν) is large and the mean heterozygosity (h) is lower than 0.2, single-locus heterozygosity is either approximately 0 or 0.5. If h increases further, however, heterozygosity shows a multiple-peak distribution. Reflecting this type of distribution, the relationship between the mean and variance of heterozygosity is considerably different from that for neutral genes. When s/v is large, the proportion of polymorphic loci increases approximately linearly with mean heterozygosity. The distribution of allele frequencies is also drastically different from that of neutral genes, and generally shows a peak at the intermediate gene frequency. Implications of these results on the maintenance of allozyme polymorphism are discussed.     

Spatial and temporal variability in cyanobacterial populations controlled by physical processes

The Fitzroy impoundment is a long slender water body (10 m deep)formed by the regulation of the Fitzroy River in tropical Australia.Large, monsoonally driven discharges in late summer flush theimpoundment repeatedly leaving, after 2 months, a longitudinallyuniform, well-mixed water column, rich in dissolved nutrientsand with high turbidity. For the rest of the year flows arenegligible. Paradoxically, two sites with initially identicalnutrient and stratification characteristics, and located only30 km apart, develop quite different patterns of cyanobacterialsuccession. The upstream site is initially dominated by Anabaenacircinalis which appears in early spring and collapses withinthe month. A mixed population of Anabaenopsis elenkinii andAphanizomenon issatschenkoi then develops at both sites. Thisis followed by a mixture of small cyanobacteria (consistingof Cylindrospermopsis, Planktolyngbya and Limnothrix) whichdevelops mainly at the downstream site and persists for 3 monthsuntil flushed away by flood flows. We report on data coveringan 8 month period of investigation of the stratification, lightclimate, temperature and nutrient dynamics at these two sites.We show that large-scale climatic conditions and the local weatherpattern set the physical and chemical conditions which determinethe cyanobacterial response.     

Beta 2 microglobulin in normal populations and populations at risk

Quantitative analysis of beta-2-microglobulin (beta-2-M) may be a useful test for early diagnosis of acquired immuno-deficiency syndrome (AIDS). Even if beta-2-M is an unspecific marker, 96% of 45 patients with confirmed AIDS and 82% of 45 patients with lymphadenopathy have excessive (3 mg/l) beta-2-M value. beta-2-M is also useful in epidemiological studies, especially in subjects in close contact with patients, and in polytransfused hemophiliacs. At last, beta-2-M may be useful as a screening method in blood banks: from a study of 929 sera, excessive beta-2-M value was observed in 16 cases, which were excluded as blood donors.     

Discovery of rare mutations in populations: TILLING by sequencing

Discovery of rare mutations in populations requires methods, such as TILLING (for Targeting Induced Local Lesions in Genomes), for processing and analyzing many individuals in parallel. Previous TILLING protocols employed enzymatic or physical discrimination of heteroduplexed from homoduplexed target DNA. Using mutant populations of rice (Oryza sativa) and wheat (Triticum durum), we developed a method based on Illumina sequencing of target genes amplified from multidimensionally pooled templates representing 768 individuals per experiment. Parallel processing of sequencing libraries was aided by unique tracer sequences and barcodes allowing flexibility in the number and pooling arrangement of targeted genes, species, and pooling scheme. Sequencing reads were processed and aligned to the reference to identify possible single-nucleotide changes, which were then evaluated for frequency, sequencing quality, intersection pattern in pools, and statistical relevance to produce a Bayesian score with an associated confidence threshold. Discovery was robust both in rice and wheat using either bidimensional or tridimensional pooling schemes. The method compared favorably with other molecular and computational approaches, providing high sensitivity and specificity.     

Genetic variation of pine in natural Crimean populations and in artificial populations in Krivbass

The comparative analysis of the genetic variation in the plantations of Pinus pallasiana D. Don in Krivbass and the Crimean populations has been conducted using the electrophoretic division of isoenzymes of 10 geneenzymous systems, encoded by 23 loci. In the artificial plantations of industrial ecotopes of Krivbass the level of genetic variation has been higher than in natural stands of Pinus pallasiana D. Don. within the range of one microslope in the Mountainous Crimea. The Nei' s genetic distance (Dn) between two regions varied within 0.016 to 0.026.