Detection of genes for membrane-bound nitrate reductase in nitrate-respiring bacteria and in community DNA

A nested PCR primed by four degenerate oligonucleotides was developed for the specific amplification of sequences from the narG gene encoding the membrane-bound nitrate reductase. This approach was used to amplify fragments of the narG gene from five Pseudomonas species previously shown to be able to express the membrane-bound nitrate reductase and from community DNA extracted from a freshwater sediment. Amino acid sequences encoded by the narG fragments were compared to one another, and to the corresponding regions of related enzymes. This comparison indicates that the amplification protocols are specific for their intended targets. Sequences amplified from community DNA were tightly clustered, which may indicate a degree of homogeneity in the sediment community. The PCR primers and amplification protocols described will be useful in future studies of nitrate respiring populations.     

Record Dynamics in Ants

The success of social animals (including ourselves) can be attributed to efficiencies that arise from a division of labour. Many animal societies have a communal nest which certain individuals must leave to perform external tasks, for example foraging or patrolling. Staying at home to care for young or leaving to find food is one of the most fundamental divisions of labour. It is also often a choice between safety and danger. Here we explore the regulation of departures from ant nests. We consider the extreme situation in which no one returns and show experimentally that exiting decisions seem to be governed by fluctuating record signals and ant-ant interactions. A record signal is a new ‘high water mark’ in the history of a system. An ant exiting the nest only when the record signal reaches a level it has never perceived before could be a very effective mechanism to postpone, until the last possible moment, a potentially fatal decision. We also show that record dynamics may be involved in first exits by individually tagged ants even when their nest mates are allowed to re-enter the nest. So record dynamics may play a role in allocating individuals to tasks, both in emergencies and in everyday life. The dynamics of several complex but purely physical systems are also based on record signals but this is the first time they have been experimentally shown in a biological system.     

Oligomeric states of bacteriophage T7 gene 4 primase/helicase

Electron microscopic and crystallographic data have shown that the gene 4 primase/helicase encoded by bacteriophage T7 can form both hexamers and heptamers. After cross-linking with glutaraldehyde to stabilize the oligomeric protein, hexamers and heptamers can be distinguished either by negative stain electron microscopy or electrophoretic analysis using polyacrylamide gels. We find that hexamers predominate in the presence of either dTTP or beta,gamma-methylene dTTP whereas the ratio between hexamers and heptamers is nearly the converse in the presence of dTDP. When formed, heptamers are unable to efficiently bind either single-stranded DNA or double-stranded DNA. We postulate that a switch between heptamer to hexamer may provide a ring-opening mechanism for the single-stranded DNA binding pathway. Accordingly, we observe that in the presence of both nucleoside di- and triphosphates the gene 4 protein exists as a hexamer when bound to single-stranded DNA and as a mixture of heptamer and hexamer when not bound to single-stranded DNA. Furthermore, altering regions of the gene 4 protein postulated to be conformational switches for dTTP-dependent helicase activity leads to modulation of the heptamer to hexamer ratio.     

Arboreal arthropod biodiversity in woodlands. II. The pattern of recovery of diversity on Melaleuca linariifolia following defaunation

This study examines the level of isolation of arthropod faunas present on specimens of the endemic woodland tree Melaleuca linariifolia by investigating the recovery of faunas after defaunation using insecticide. One tree from each of 21 pairs of trees was sprayed at the beginning of the project (early April 1994). After predetermined periods, three test trees were resprayed along with matched control trees. A total of 95 154 arthropods were collected and sorted during the project. The number of species present on the trees recovered within 16 weeks of spraying, with common species recolonizing within a fortnight. The rarer species both of mobile (Diptera) and relatively sedentary (Araneae) taxa reappeared at similar rates. Complete recovery of numbers occurred by week 8 after spraying. Evenness (as Simpson’s D) recovered over the first 2 months; however, both the number of individuals and the evenness continued to diverge from the pattern seen on the control trees until the end of the study. While the rate of movement of individuals and species was such as to provide an apparently complete set of replacement species within several months of perturbation, the structure of the community found on the trees was still seriously disrupted after 1 year. Comparison of the suites of species originally found on the trees with those found in the respray samples and the control samples showed that the set of colonizing species was no more similar to the original fauna of the tree than it was to those on the control tree. The relatively rapid colonization of the trees by a suite of rare species – not necessarily those that were on particular trees before perturbation – indicates that rarity was due neither to inability of the species to colonize the trees nor to the suitability of the trees for these species. Recovery of rare species was to a level similar to that found on the control trees. That the divergences from the controls continued (in number of individuals and in evenness), implies a definite connection between the different faunas of a tree and their partial isolation from fauna communities on other trees. Whatever the forces that maintain suites of species on each tree, it is not the ability of the species to reach and colonize trees, nor certain attributes of a tree, that make it suitable only for a particular subset of the species available. Trees are not isolated entities but neither are they part of a fully integrated community, either chronologically or spacially, and issues of scale are also likely to be important in understanding and estimating the dynamics and factors regulating biodiversity levels.     

A comparative study of phenotypic traits related to resource utilization in anuran communities

Larval anuran communities vary along a gradient of pond permanency. The families Hylidae, Ranidae, and Bufonidae have each diversified into multiple pond types. Species using ponds that dry seasonally (vernal ponds) must compete well to metamorphose before pond drying, while permanent ponds, which contain more predators, produce weaker selection for competitive ability. Quantifying phenotypic traits related to resource acquisition in 14 anuran species provides insight into the mechanistic underpinnings of adaptive radiation in anuran lineages. Under controlled laboratory conditions and at both early and late developmental stages, relative growth rate, relative consumption rate, assimilation efficiency and production efficiency varied significantly among species. As predicted, vernal pond species had high growth rates relative to species using more than one pond type. However, within a pond type, families frequently differed in phenotype. In species using permanent ponds with fish predators, hylids had high growth rates while ranids had low growth rates, and in species using vernal ponds, bufonids had higher assimilation efficiencies than hylids. Differences also occurred between stages; hylids and ranids in permanent, but fishless, ponds were similar at an early stage, but late stage hylids in the same pond type had lower growth and consumption rates, and higher assimilation efficiencies than ranids. Functional relationships between phenotypic traits also differed among species and developmental stage. Negative correlations between evolutionary change (independent contrast values) in both mass and growth rate (both stages), and mass and consumption rate (late stage), suggest the presence of trade-offs. These results indicate that different lineages have diversified in different ways into the same pond types.     

Quantification of mussel (Mytilus edulis) growth from power station cooling waters in response to chlorination procedures

The age and growth history of individual mussels collected from the cooling water culverts of a power station were determined from the growth bands present in acetate peels of polished and etched shell sections. During periods of exposure to the antifouling agent, sodium hypochlorite (0.2mgl^‐1), shell growth was severely reduced, resulting in marked changes in the structure and deposition of the shell. As a consequence of chlorination, the growth rate of the mussel population occurring within the culverts was substantially lower and the mean length‐at‐age significantly smaller than that of a naturally occurring population immediately outside the cooling water intake. The growth patterns present in the shells of mussels experimentally added to the cooling waters during chlorination were compared with, and found to be similar to, the patterns in the shells of mussels that had settled naturally in the culverts. The daily growth of the experimentally exposed mussels (1.1–5.2 μm d^‐1) is two orders of magnitude lower than the growth rate of mussels growing in untreated waters. The use of mussels for evaluating the efficiency and long‐term effects of low level chlorination is discussed.     

Terrestrial biosphere models need better representation of vegetation phenology: results from the North American Carbon Program Site Synthesis

Phenology, by controlling the seasonal activity of vegetation on the land surface, plays a fundamental role in regulating photosynthesis and other ecosystem processes, as well as competitive interactions and feedbacks to the climate system. We conducted an analysis to evaluate the representation of phenology, and the associated seasonality of ecosystem‐scale CO₂ exchange, in 14 models participating in the North American Carbon Program Site Synthesis. Model predictions were evaluated using long‐term measurements (emphasizing the period 2000–2006) from 10 forested sites within the AmeriFlux and Fluxnet‐Canada networks. In deciduous forests, almost all models consistently predicted that the growing season started earlier, and ended later, than was actually observed; biases of 2 weeks or more were typical. For these sites, most models were also unable to explain more than a small fraction of the observed interannual variability in phenological transition dates. Finally, for deciduous forests, misrepresentation of the seasonal cycle resulted in over‐prediction of gross ecosystem photosynthesis by +160 ± 145 g C m^?2 yr^?1 during the spring transition period and +75 ± 130 g C m^?2 yr^?1 during the autumn transition period (13% and 8% annual productivity, respectively) compensating for the tendency of most models to under‐predict the magnitude of peak summertime photosynthetic rates. Models did a better job of predicting the seasonality of CO₂ exchange for evergreen forests. These results highlight the need for improved understanding of the environmental controls on vegetation phenology and incorporation of this knowledge into better phenological models. Existing models are unlikely to predict future responses of phenology to climate change accurately and therefore will misrepresent the seasonality and interannual variability of key biosphere–atmosphere feedbacks and interactions in coupled global climate models.