Mutational divergence of life-history traits in an obligate parthenogen.

Three lines of obligately parthenogenetic Daphnia were allowed to diverge for a 4-year period (approximately 150 generations) with mutation as the sole source of variability. Life-history traits and morphological characters were then surveyed for between-line differences. Significant divergence was found with respect to both number and size of offspring, with no difference in total offspring biomass. No significant differences were found in any of the other characters. These results confirm the hypothesis that purely asexual lines can accumulate enough polygenic variation via mutation to support potentially adaptive changes on a microevolutionary time scale.     

Population dynamics of obligate cooperators

Obligate cooperative breeding species demonstrate a high rate of group extinction, which may be due to the existence of a critical number of helpers below which the group cannot subsist. Through a simple model, we study the population dynamics of obligate cooperative breeding species, taking into account the existence of a lower threshold below which the instantaneous growth rate becomes negative. The model successively incorporates (i) a distinction between species that need helpers for reproduction, survival or both, (ii) the existence of a migration rate accounting for dispersal, and (iii) stochastic mortality to simulate the effects of random catastrophic events. Our results suggest that the need for a minimum number of helpers increases the risk of extinction for obligate cooperative breeding species. The constraint imposed by this threshold is higher when helpers are needed for reproduction only or for both reproduction and survival. By driving them below this lower threshold, stochastic mortality of lower amplitude and/or lower frequency than for non-cooperative breeders may be sufficient to cause the extinction of obligate cooperative breeding groups. Migration may have a buffering effect only for groups where immigration is higher than emigration; otherwise (when immigrants from nearby groups are not available) it lowers the difference between actual group size and critical threshold, thereby constituting a higher constraint.     

Population and life-history consequences of within-cohort individual variation

The consequences of within-cohort (i.e., among-individual) variation for population dynamics are poorly understood, in particular for the case where life history is density dependent. We develop a physiologically structured population model that incorporates individual variation among and within cohorts and allows us to explore the intertwined relationship between individual life history and population dynamics. Our model is parameterized for the lizard Zootoca vivipara and reproduces well the species' dynamics and life history. We explore two common mechanisms that generate within-cohort variation: variability in food intake and variability in birth date. Predicted population dynamics are inherently very stable and do not qualitatively change when either of these sources of individual variation is introduced. However, increased within-cohort variation in food intake leads to changes in morphology, with longer but skinnier individuals, even though mean food intake does not change. Morphological changes result from a seemingly universal nonlinear relationship between growth and resource availability but may become apparent only in environments with strongly fluctuating resources. Overall, our results highlight the importance of using a mechanistic framework to gain insights into how different sources of intraspecific variability translate into life-history and population-dynamic changes.     

Artificial habitats and the restoration of degraded marine ecosystems and fisheries

Artificial habitats in marine ecosystems are employed on a limited basis to restore degraded natural habitats and fisheries, and more extensively for a broader variety of purposes including biological conservation and enhancement as well as social and economic development. Included in the aims of human-made habitats classified as artificial reefs are: Aquaculture/marine ranching; promotion of biodiversity; mitigation of environmental damage; enhancement of recreational scuba diving; eco-tourism development; expansion of recreational fishing; artisanal and commercial fisheries production; protection of benthic habitats against illegal trawling; and research. Structures often are fabricated according to anticipated physical influences or life history requirements of individual species. For example, many of the world’s largest reefs have been deployed as part of a national fisheries program in Japan, where large steel and concrete frameworks have been carefully designed to withstand strong ocean currents. In addition, the differing ecological needs of porgy and sea bass for shelter guided the design of the Box Reef in Korea as a device to enhance productivity of marine ranching. The effect of these and other structures on fisheries catch is positive. But caution must be exercised to avoid using reefs simply as fishing devices to heavily exploit species attracted to them. No worldwide database for artificial habitats exists.The challenge to any ecological restoration effort is to define the condition or possibly even the historic baseline to which the system will be restored; in other words, to answer the question: “Restoration to what?” Examples of aquatic ecosystem restoration from Hong Kong (fisheries), the Pacific Ocean (kelp beds), Chesapeake Bay (oysters) and the Atlantic Ocean (coral reefs) are discussed. The degree to which these four situations consider or can approach a baseline is indicated and compared (e.g., four plants per 100 m² are proposed in one project). Measurement of performance is a key factor in restoration planning. These situations also are considered for the ecosystem and fishery contexts in which they are conducted. All use ecological data as a basis for physical design of restoration structures. The use of experimental, pilot and modeling practices is indicated.A context for the young field of marine restoration is provided by reviewing major factors in ecosystem degradation, such as high stress on 70% of commercially valuable fishes worldwide. Examples of habitat disruption include an extensive hypoxic/anoxic zone in the Gulf of Mexico and nutrient and contaminant burdens in the North Sea. Principles of ecological restoration are summarized, from planning through to evaluation. Alternate approaches to facilitate ecological recovery include land-use and ecosystem management and determining levels of human population, consumption and pollution.     

Population differentiation in the life-history characteristics of salt-marsh annuals

Coastal salt marshes are heterogeneous spatially but predictable temporally. Genetic differentiation between populations on different parts of a marsh in response to this combination of circumstances has been well documented in several perennial species; differentiation has been evident in certain features of the life cycle that contribute to overall fitness. Our studies of the annuals in the marshes of the north Norfolk coast of Britain have shown that there are distinct populations, that have particular micro-habitats and different vegetational affinities, within the annual species Suaeda maritima and within the complex of several closely related species of Salicornia. Consequently, three sequential questions about these annuals may be posed: 1. What is the extent of genetic differentiation? 2. What features of the life history show differentiation? 3. Can any of this variation be demonstrated to have adaptive value? This paper reviews evidence for the upper- and lower-marsh populations of (diploid) Salicornia europaea agg. at Stiffkey, U.K. The six main approaches described comprise collateral cultivation, perturbation of the field environment, isozyme analysis and three types of reciprocal transplantation. The value of these complementary methods is discussed, and they are used to demonstrate that there is considerable genetic differentiation between the two populations; it is manifested in the phenology of growth, mortality and density-dependent fecundity. In terms of the ability of individuals to leave descendants, there is a dramatic reduction in fitness of each population when it is grown in the reciprocal environment. This finding indicates that the genetic differentiation has clear adaptive value.     

Oxidatively denatured proteins are degraded by an ATP-independent proteolytic pathway in Escherichia coli

E. coli contains a soluble proteolytic pathway which can recognize and degrade oxidatively denatured proteins and protein fragments, and which may act as a "secondary antioxidant defense." We now provide evidence that this proteolytic pathway is distinct from the previously described ATP-dependent, and protease "La"-dependent, pathway which may degrade other abnormal proteins. Cells (K12) which were depleted of ATP, by arsenate treatment or anaerobic incubation (after growth on succinate), exhibited proteolytic responses to oxidative stress which were indistinguishable from those observed in cells with normal ATP levels. Furthermore, the proteolytic responses to oxidative damage by menadione or H2O2 were almost identical in the isogenic strains RM312 (a K12 derivative) and RM1385 (a lon deletion mutant of RM312). Since the lon (or capR) gene codes for the ATP-dependent protease "La," these results indicate that neither ATP nor protease "La" are required for the degradation of oxidatively denatured proteins. We next prepared cell-free extracts of K12, RM312, and RM1385 and tested the activity of their soluble proteases against proteins (albumin, hemoglobin, superoxide dismutase, catalase) which had been oxidatively denatured (in vitro) by exposure to .OH, .OH + O2- (+O2), H2O2, or ascorbate plus iron. The breakdown of oxidatively denatured proteins was several-fold higher than that of untreated proteins in extracts from all three strains, and ATP did not stimulate degradation. Incubation of extracts at 45 degrees C, which inactivates protease "La," actually stimulated the degradation of oxidatively denatured proteins. Although Ca2+ had little effect on proteolysis, serine reagents, transition metal chelators, and hemin effectively inhibited the degradation of oxidatively denatured proteins in both intact cells and cell-free extracts. Degradation of oxidatively denatured proteins in cell-free extracts was maximal at pH 7.8, and was unaffected by dialysis of the extracts against membranes with molecular weight cutoffs as high as 50,000. Our results indicate the presence of a neutral, ATP- and calcium- independent proteolytic pathway in the E. coli cytosol, which contains serine- and metallo- proteases (with molecular weights greater than 50,000), and which preferentially degrades oxidatively denatured proteins.     

Population dynamics and the ecological stability of obligate pollination mutualisms

Mutualistic interactions almost always produce both costs and benefits for each of the interacting species. It is the difference between gross benefits and costs that determines the net benefit and the per-capita effect on each of the interacting populations. For example, the net benefit of obligate pollinators, such as yucca and senita moths, to plants is determined by the difference between the number of ovules fertilized from moth pollination and the number of ovules eaten by the pollinator's larvae. It is clear that if pollinator populations are large, then, because many eggs are laid, costs to plants are large, whereas, if pollinator populations are small, gross benefits are low due to lack of pollination. Even though the size and dynamics of the pollinator population are likely to be crucial, their importance has been neglected in the investigation of mechanisms, such as selective fruit abortion, that can limit costs and increase net benefits. Here, we suggest that both the population size and dynamics of pollinators are important in determining the net benefits to plants, and that fruit abortion can significantly affect these. We develop a model of mutualism between populations of plants and their pollinating seed-predators to explore the ecological consequences of fruit abortion on pollinator population dynamics and the net effect on plants. We demonstrate that the benefit to a plant population is unimodal as a function of pollinator abundance, relative to the abundance of flowers. Both selective abortion of fruit with eggs and random abortion of fruit, without reference to whether they have eggs or not, can limit pollinator population size. This can increase the net benefits to the plant population by limiting the number of eggs laid, if the pollination rate remains high. However, fruit abortion can possibly destabilize the pollinator population, with negative consequences for the plant population.     

Prevalence and diversity patterns of avian blood parasites in degraded African rainforest habitats

Land use changes including deforestation, road construction and agricultural encroachments have been linked to the increased prevalence of several infectious diseases. In order to better understand how deforestation affects the prevalence of vector-borne infectious diseases in wildlife, nine paired sites were sampled (disturbed vs. undisturbed habitats) in Southern Cameroon. We studied the diversity, prevalence and distribution of avian malaria parasites ( Plasmodium spp.) and other related haemosporidians (species of Haemoproteus and Leucocytozoon ) from these sites in two widespread species of African rainforest birds, the yellow-whiskered greenbul ( Andropadus latirostris , Pycnonotidae) and the olive sunbird ( Cyanomitra olivacea , Nectariniidae). Twenty-six mitochondrial cytochrome b lineages were identified: 20 Plasmodium lineages and 6 Haemoproteus lineages. These lineages showed no geographic specificity, nor significant differences in lineage diversity between habitat types. However, we found that the prevalence of Leucocytozoon and Haemoproteus infections were significantly higher in undisturbed than in deforested habitats ( Leucocytozoon spp. 50.3% vs. 35.8%, Haemoproteus spp. 16.3% vs. 10.8%). We also found higher prevalence for all haemosporidian parasites in C. olivacea than in A. latirostris species (70.2% vs. 58.2%). Interestingly, we found one morphospecies of Plasmodium in C. olivacea , as represented by a clade of related lineages, showed increased prevalence at disturbed sites, while another showed a decrease, testifying to different patterns of transmission, even among closely related lineages of avian malaria, in relation to deforestation. Our work demonstrates that anthropogenic habitat change can affect host–parasite systems and result in opposing trends in prevalence of haemosporidian parasites in wild bird populations.     

Nature of the inactivation of the isocitrate dehydrogenase from an obligate halophile

The nicotinamide adenine dinucleotide phosphate-specific isocitrate dehydrogenase (ICDH) of Halobacterium cutirubrum is rapidly inactivated at low NaCl levels. From sucrose gradient analysis, it was estimated that the active ICDH has an S(20,w) of 5.3 and a molecular weight of 75,000. The inactivation by removal of NaCl causes an unfolding of the protein yielding a less-compact conformer with an S(20,w) of 2.0. This inactivation apparently causes internal sulfhydryl groups to be exposed. Over 90% of the initial activity can be restored by dialyzing the inactivated ICDH against 4 m NaCl, provided that the exposed sulfhydryl groups are protected with dithiothreitol. The ICDH is permanently inactivated when the sulfhydryl groups are oxidized or alkylated. The alkylation of the inactive ICDH was demonstrated by treatment with (14)C-N-ethyl maleimide. Sucrose gradient analysis showed that (14)C was bound to a protein with sedimentation properties identical to that of reversibly inactivated ICDH, i.e., an S(20,w) of 2.0. Much less (14)C was bound when active ICDH was treated with (14)C-N-ethyl maleimide. The H. cutirubrum ICDH resembles other bacterial isocitrate dehydrogenases in being susceptible to concerted feedback inhibition by oxalacetate and glyoxalate.     

Characterization of Symbiobacterium toebii, an obligate commensal thermophile isolated from compost

A symbiotic thermophilic bacterium, strain SC-1, was isolated from hay compost (toebi) in Korea. The new isolate exhibited an obligate commensal interaction with a thermophilic Geobacillus strain and required crude extracts and/or culture supernatant from Geobacillus sp. SK-1 for axenic growth. The growth factors from Geobacillus sp. SK-1 were irreversibly inactivated by phenol or protease treatment, suggesting that they might be proteins. The cells of strain SC-1 were non-spore forming, nonmotile rods that were stained Gram-negatively. The isolate was a microaerophilic heterotroph. Growth was observed between 45 degrees and 70 degrees C (optimum: 60 degrees C; 2.4-h doubling time) and pH 6.0 and 9.0 (optimum: pH 7.5). The G+C content of the genomic DNA was 65 mol%, and the major quinones were MK-6 and MK-7. A phylogenetic analysis of its 16S rDNA sequence indicated that strain SC-1 is closely related to Symbiobacterium thermophilum and so was named Symbiobacterium toebii on the basis of its physiological and molecular properties.     

Development of an obligate anaerobe specific biocide

Summary Anaerobic bacteria, such as sulfate-reducing bacteria and clostridia, are capable of generating H₂S and organic acids which corrode metallurgy resulting in millions of dollars of damage to industry annually. The bacteria are obligate anaerobes which grow typically on equipment surfaces under deposits such as biofilms. A successful method of penetrating biofilm and killing the anaerobic bacteria specifically has not been previously presented. We have investigated whether a blend of 1-(2-hydroxyethyl)-2-methyl-5-nitroimidazole (metronidazole) and a biodispersant would killDesulfovibrio, Desulfotomaculum, andClostridium species grown in the laboratory and in field applications. We found the blend significantly reduced the anaerobes in laboratory cultures. However, in a bioreactor designed to induced a high level of biofilm production and enhance underdeposit growth of anaerobic bacteria, a 40–58% increase in the antibiotic-biodispersant blend concentration was required. The metronidazole blend killed obligate anaerobic bacteria specifically but was non-toxic to aerobic bacteria and fungi. These results were confirmed in cooling tower field trial studies.     

Mutagenesis resulting from depurination is an SOS process

When bacteriophage phi X174 am3 DNA depurinated in vitro is transfected into E. coli spheroplasts prepared from bacteria previously exposed to UV light, a strong mutagenic response is observed. This mutagenic response does not occur in spheroplasts derived from pre-irradiated bacteria carrying defective recA, recF or umuC genes. These findings indicate that mutagenesis at apurinic sites is an SOS-dependent process. The mutagenic response is not dependent on the multiplicity of transfection. This suggests that mutagenesis is not mediated by recombination.     

Bluehead chub nesting activity: a potential mechanism of population persistence in degraded stream habitats

Aquatic biodiversity continues to decline as humans modify the landscape, mainly because of stream habitat alterations and loss caused by urban development. Bluehead chubs may mitigate some effects of instream habitat degradation by providing clean gravel substrate via their spawning nests. We used path analysis, an extension of multiple linear regression, to explore the relationships among instream habitat degradation, adult chub abundance, chub nesting activity, and chub reproductive performance. Age-0 chub abundance was best explained by small adult abundance and nest abundance. Habitat disturbance indirectly and negatively influenced age-0 chub abundance through adult chubs and nest abundance. Percentages of pool and run habitat also had indirect negative effects on age-0 chub abundance. Several metrics of chub nesting activity (nest density [proportion of substrate occupied by nests], average nest size, and number of nests) were explained by both adult chub abundance and nesting site conditions. Variability among stream systems described significant variation in adult chub abundance and nesting characteristics and, if unaccounted for, would have resulted in large unexplained variability. Chub nesting activity served as a link between habitat degradation, adult chub abundance, and their reproductive performance. Our study provides preliminary evidence that bluehead chubs’ nesting activity may be a mechanism of their persistence in degraded stream reaches. We recommend confirmatory studies through in-stream manipulative experiments.     

Characterization of the L-lysine biosynthetic pathway in the obligate methylotroph Methylophilus methylotrophus

The L-lysine biosynthetic pathway of the gram-negative obligate methylotroph Methylophilus methylotrophus AS1 was examined through characterization of the enzymes aspartokinase (AK), aspartsemialdehyde dehydrogenase, dihydrodipicolinate synthase (DDPS), dihydrodipicolinate reductase, and diaminopimelate decarboxylase. The AK was inhibited by L-threonine and by a combination of L-threonine and L-lysine, but not by L-lysine alone, and the activity of DDPS was moderately reduced by L-lysine. In an L-lysine producing mutant (G49), isolated as an S-(2-aminoethyl)-L-cysteine (lysine analog) resistant strain, both AK and DDPS were partially resistant to feedback inhibition. The ask and dapA genes encoding AK and DDPS respectively were isolated from the parental strain, AS1, and its G49 derivative. Comparison of the sequences revealed a point mutation in each of these genes in G49. The mutation in the ask gene altered aspartic acid in a key region involved in the allosteric regulation common to AKs, while a novel mutation in the dapA gene altered tyrosine-106, which was assumed to be involved in the binding of L-lysine to DDPS.     

Population genetics from an information perspective

Some basic effects of population genetics are derived governing the occurrences of alleles A(i)and genotypes A(i)A(j)among its members. A principle of extreme physical information (EPI) is used. These effects are (1) the equation of genetic change, (2) Fisher's theorem of partial change, (3) a new uncertainty principle, and (4) the monotonic decrease of Fisher information with time, indicating increased disorder for the population. General conditions of population change are allowed: fitness coefficients w(ij)generally changing with time [except in effect (2)], population randomly or non-randomly mating, and a general number of loci present within each chromosome. EPI is a practical tool for deriving probability laws. It is an outgrowth of a physical process that occurs during any act of measurement. Here the measurement is the random observation of a genotype A(i)A(j). This observation is to be used to estimate the time of the observation, called "evolutionary time". The measurement activity incurs errors in the estimated observation time and fitness value of the observed genotype. By the Cramer-Rao inequality, the product of the two uncertainties must exceed unity [effect (3)]. The Fisher information I in data space is postulated to originate in the space of the genotype where it had some generally larger value J. The EPI principle extremizes the loss of information (I--J) with I=1/2 J. The solution gives rise to effects (1) and (2). Finally, it is shown that effect (4) holds when the population approaches an equilibrium state, e.g. for time values greater than a threshold if fitness coefficients w(ij)are constant. EPI provides a common framework for deriving physical laws and laws of population genetics. The new effects (3) and (4) are confirmed through computer simulation.     

Luteimonas dalianensis sp. nov., an obligate marine bacterium isolated from seawater

A marine bacterial strain, designated OB44-3^T, was isolated from a crude oil-contaminated seawater sample collected near Dalian Bay, China. Cells of strain OB44-3^T were Gramnegative, aerobic, rod-shaped, and oxidase- and catalasepositive. The major fatty acids were branched-chain saturated iso-C_15:0 (27.9%) and unsaturated iso-C_17:1 ω9c (14.8%). The DNA G+C content was 64.6 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain OB44-3^T was a member of the genus Luteimonas (95–96% 16S rRNA gene sequence similarity); its closest neighbors were the type strains of Luteimonas terricola (96% sequence similarity), Luteimonas mephitis (96%), and Luteimonas lutimaris (96%). On the basis of phenotypic, chemotaxonomic, and phylogenetic distinctiveness, strain OB44-3^T was considered to represent a novel species of the genus Luteimonas. The name Luteimonas dalianensis sp. nov. is proposed, with strain OB44-3^T (=CGMCC 1.12191^T =JCM 18136^T) as the type strain.