Spatial patterns and coexistence mechanisms in systems with unidirectional flow

River ecosystems are the prime example of environments where unidirectional flow influences the dispersal of individuals. Spatial patterns of community composition and species replacement emerge from complex interplays of hydrological, geochemical, biological, and ecological factors. Local processes affecting algal dynamics are well understood, but a mechanistic basis for large scale emerging patterns is lacking. To understand how these patterns could emerge in rivers, we analyze a reaction-advection-diffusion model for two competitors in heterogeneous environments. The model supports waves that invade upstream up to a well-defined "upstream invasion limit". We discuss how these waves are produced and present their key properties. We suggest that patterns of species replacement and coexistence along spatial axes reflect stalled waves, produced from diffusion, advection, and species interactions. Emergent spatial scales are plausible given parameter estimates for periphyton. Our results apply to other systems with unidirectional flow such as prevailing winds or climate-change scenarios.     

Spatial Patterns of Prisoner’s Dilemma Game in Metapopulations

Because to defect is the evolutionary stable strategy in the prisoner’s dilemma game (PDG), understanding the mechanism generating and maintaining cooperation in PDG, i.e. the paradox of cooperation, has intrinsic significance for understanding social altruism behaviors. Spatial structure serves as the key to this dilemma. Here, we build the model of spatial PDG under a metapopulation framework: the sub-populations of cooperators and defectors obey the rules in spatial PDG as well as the colonization–extinction process of metapopulations. Using the mean-field approximation and the pair approximation, we obtain the differential equations for the dynamics of occupancy and spatial correlation. Cellular automaton is also built to simulate the spatiotemporal dynamics of the spatial PDG in metapopulations. Join-count statistics are used to measure the spatial correlation as well as the spatial association of the metapopulation. Simulation results show that the distribution is self-organized and that it converges to a static boundary due to the boycotting of cooperators to defectors. Metapopulations can survive even when the colonization rate is lower than the extinction rate due to the compensation of cooperation rewards for extinction debt. With a change of parameters in the model, a metapopulation can consist of pure cooperators, pure defectors, or cooperator–defector coexistence. The necessary condition of cooperation evolution is the local colonization of a metapopulation. The spatial correlation between the cooperators tends to be weaker with the increase in the temptation to defect and the habitat connectivity; yet the spatial correlation between defectors becomes stronger. The relationship between spatial structure and the colonization rate is complicated, especially for cooperators. The metapopulation may undergo a temporary period of prosperity just before the extinction, even while the colonization rate is declining. An erratum to this article can be found at     

Hydraulic design of leaves: insights from rehydration kinetics

We examined the leaf hydraulic design in 10 species based on their rehydration kinetics. In all cases, a biphasic response described the temporal pattern of water uptake, with time constants of approximately 30 to 800 s and approximately 800 to 8000 s. The time constants of the fast phase were significantly shorter in the six angiosperms (30 to 110 s) compared with the two single-veined conifer species (>400 s) examined, while the two multi-veined gymnosperm species, Gnetum gnemon and Ginkgo biloba, had time constants for the fast phase of approximately 150 s. Among angiosperm species, the fast phase constituted 50-90% of the total water absorbed, whereas in gymnosperms 70-90% of the water uptake could be assigned to the slow phase. In the four gymnosperms, the relative water uptake corresponding to the fast phase matched to a good degree the relative volume of the venation and bundle sheath extension; whereas in the angiosperm species, the relatively larger water influx during the fast phase was similar in relative volume to the combined venation, bundle sheath extension, epidermis and (in four species) the spongy mesophyll. This suggests a general trend from a design in which the epidermis is weakly connected to the veins (all four gymnosperms), to a design with good hydraulic connection between epidermis and veins that largely bypasses the mesophyll (four of six angiosperms), to a design in which almost the entire leaf appears to function as a single pool.     

Evidence for an interaction between the SH3 domain and the N-terminal extension of the essential light chain in class II myosins

The function of the src-homology 3 (SH3) domain in class II myosins, a distinct beta-barrel structure, remains unknown. Here, we provide evidence, using electron cryomicroscopy, in conjunction with light-scattering, fluorescence and kinetic analyses, that the SH3 domain facilitates the binding of the N-terminal extension of the essential light chain isoform (ELC-1) to actin. The 41 residue extension contains four conserved lysine residues followed by a repeating sequence of seven Pro/Ala residues. It is widely believed that the highly charged region interacts with actin, while the Pro/Ala-rich sequence forms a rigid tether that bridges the approximately 9 nm distance between the myosin lever arm and the thin filament. In order to localize the N terminus of ELC in the actomyosin complex, an engineered Cys was reacted with undecagold-maleimide, and the labeled ELC was exchanged into myosin subfragment-1 (S1). Electron cryomicroscopy of S1-bound actin filaments, together with computer-based docking of the skeletal S1 crystal structure into 3D reconstructions, showed a well-defined peak for the gold cluster near the SH3 domain. Given that SH3 domains are known to bind proline-rich ligands, we suggest that the N-terminal extension of ELC interacts with actin and modulates myosin kinetics by binding to the SH3 domain during the ATPase cycle.     

An ATP hydrolysis sensor in the DNA packaging motor from bacteriophage T4 suggests an inchworm-type translocation mechanism

Tailed bacteriophages and large eukaryotic viruses employ powerful molecular motors to translocate dsDNA into a preassembled capsid shell. The phage T4 motor is composed of a dodecameric portal and small and large terminase subunits assembled at the special head-tail connector vertex of the prohead. The motor pumps DNA through the portal channel, utilizing ATP hydrolysis energy provided by an ATPase present in the large terminase subunit. We report that the ATPase motors of terminases, helicases, translocating restriction enzymes, and protein translocases possess a common coupling motif (C-motif). Mutations in the phage T4 terminase C-motif lead to loss of stimulated ATPase and DNA translocation activities. Surprisingly, the mutants can catalyze at least one ATP hydrolysis event but are unable to turn over and reset the motor. This is the first report of a catalytic block in translocating ATPase motor after ATP hydrolysis occurred. We suggest that the C-motif is an ATP hydrolysis sensor, linking product release to mechanical motion. A novel terminase-driven mechanism is proposed for translocation of dsDNA in viruses.     

Temporal and spatial trends in nitrogen and phosphorus inputs to the watershed of the Altamaha River,Georgia, USA

The watershed of the Altamaha River, Georgia, is one of the largest in the southeastern U.S., draining 36,718 km² (including parts of metro Atlanta). We calculated both nitrogen (fertilizer, net food and feed import, atmospheric deposition, and biological N fixation in agricultural and forest lands) and phosphorus (fertilizer and net food and feed import) inputs to the watershed for 6 time points between 1954 and 2002. Total nitrogen inputs rose from 1,952 kg N km⁻² yr⁻¹ in 1954 to a peak of 3,593 kg N km⁻² yr⁻¹ in 1982 and then declined to 2,582 kg N km⁻² yr⁻¹ by 2002. Phosphorus inputs rose from 409 kg P km⁻² yr⁻¹ in 1954 to 532 kg P km⁻² yr⁻¹ in 1974 before declining to 412 kg P km⁻² yr⁻¹ in 2002. Fertilizer tended to be the most important input of both N and P to the watershed, although net food and feed import increased in importance over time and was the dominant source of N input by 2002. When considered on an individual basis, fertilizer input tended to be highest in the middle portions of the watershed (Little and Lower Ocmulgee and Lower Oconee sub-watersheds) whereas net food and feed imports were highest in the upper reaches (Upper Oconee and Upper Ocmulgee sub-watersheds). Although the overall trend in recent years has been towards decreases in both N and P inputs, these trends may be offset due to continuing increases in animal and human populations.     

Changes in the spatial variation of soil properties following shifting cultivation in a Mexican tropical dry forest

The role of secondary vegetation in restoring soil fertility during shifting cultivation in the tropics is well known. Yet the effect of secondary succession on the spatial patterns of soil properties has received little attention. To determine whether changes in the plant community as a result of shifting cultivation affect the scale of spatial dependence for biologically important soil nutrients, we sampled three dry tropical forest stands in Campeche, Mexico. These stands represented a gradient of cultivation history: one mature forest stand, a forest fallow that had undergone one cultivation-fallow cycle, and a forest fallow that had undergone two cultivation-fallow cycles. We used an analysis of semivariance to quantify the scale and magnitude of spatial dependence for organic matter content (OM), phosphorus (P), potassium (K), and aluminum (Al) in each stand. The scale of spatial dependence varied with cultivation history, but the degree of spatial dependence did not differ among stands. In the mature forest P and K were autocorrelated over distances >7.5 m. In the forest fallows 48–88% of the variation in soil P and K was autocorrelated over distances up to 1.1–5.1 m. In contrast, the range of autocorrelation for Al (∼2.5 m) did not differ among stands. We conclude that shifting cultivation changes the range of autocorrelation for biologically important soil nutrients at a scale that may influence plant growth. The finer scaled pattern of soil nutrients in forest fallows is likely to persist with continued shifting cultivation, since fallows are cleared every 3–15 years.     

Bioaugmentation and coexistence of two functionally similar bacterial strains in aerobic granules

The survival of the inoculated microbial culture is critical for successful bioaugmentation but impossible to predict precisely. As an alternative strategy, bioaugmentation of a group of microorganisms may improve reliability of bioaugmentation. This study evaluated simultaneous bioaugmentation of two functionally similar bacterial strains in aerobic granules. The two strains, Pandoraea sp. PG-01 and Rhodococcus erythropolis PG-03, showed high phenol degradation and growth rates in phenol medium, but they were characterized as having a poor aggregation activity and weak bioflocculant-producing and biofilm-forming abilities. In the spatially homogeneous batch conditions, strain PG-01 with higher growth rates outcompeted strain PG-03. However, the two strains could stably coexist in the spatially heterogeneous conditions. Then the two strains were mixed and bioaugmented into activated sludge in two sequencing batch reactors, which were operated with the different settling times of 5 and 30 min, respectively. Aerobic granules were developed only in the reactor with a settling time of 5 min. Fluorescence in situ hybridization and denaturing gradient gel electrophoresis showed that the two strains could coexist in aerobic granules but not in activated sludge. These findings suggested that the compact structure of aerobic granules provided spatial isolation for coexistence of competitively superior and inferior strains with similar functions.     

中国云南塔城滇金丝猴的社会结构

在云南塔城附近的山地森林中,我们利用摄象机记录了一群滇金丝猴通过山谷和在水源地饮水的过程。我们利用这些记录分析这群滇金丝猴的种群大小、组成成员以及个体的空间分布,并利用连续通过个体之间的时间间隔来揭示社会结构。塔城滇金丝猴群由366个个体组成,是目前所知最大的滇金丝猴群体。猴群内雌性个体较多。猴群可以分为26个单位,其中有19个单雄多雌单位、5个多雄多雌单位和2个全雄单位。统计结果表明单位内个体间的时间间隔显著比单位间的短。2/3以上的亚成年雄性个体和全雄单位一起活动。猴群在地面活动时全雄单位位于猴群的外围,充当前卫和后卫。塔城猴群的生命表组成结构与吾牙普亚猴群的大致一样,同样是多层社会结构,单雄多雌和全雄单位构成猴群的主体。亚成年雄性多数与全雄单位一起活动,表明雄性可能会从其出生的单雄多雌单位中迁移出来。     

Spatial dynamics,social norms,and the opportunity of the commons

The most important message of Levin (Ecol Res 21:328–333, 2006) is that “Ecologists and economists have much incentive for interaction.” Recent studies that account for evolutionary processes and local interactions support this view by obtaining results that run counter to conventional wisdom within resource economics. A second major message of the article is that to meet environmental challenges, humanity must develop social norms that enhance cooperative responses. Successful examples of resource management systems back up norms with economic incentives: rewards for good behavior and punishments for bad. Economic incentives are especially important if rapid and large changes in human behavior are desired.