Stochastic determinants of assemblage patterns in coral reef fishes: a quantification by means of two models

Synopsis One perspective emphasizing the importance of stochastic processes in determining coral reef fish assemblages implies that there is little organization in species richness, abundance structure, and spatial distribution. We examine the degree to which this perspective is correct by analyzing distribution of fishes on a collection of patch reefs (Discovery Bay, Jamaica). We ask the question whether these patches accumulate species and individuals in a manner consistent with stochastic expectations. To address this question we use two conceptual models, each permitting a different insight. One assumes that fish are distributed stochastically on patches while the other assumes presence of restrictions on fish distribution due to habitat structure. For each conceptual model we use two types of benchmark: we compare observed patterns to those predicted by theoretical models, and we also compare observed patterns to those obtained from a random reallocation of fish individuals to patches. We found that the conceptual model assuming stochastic processes appeared to provide weaker explanation of patterns than the conceptual model that includes restrictions due to habitat structure. Further, and more importantly, we found that (i) the community is shaped by a mixture of stochastic and non-stochastic mechanisms, and (ii) the stochastic assembly processes decrease in importance for species restricted to fewer microhabitat types and sites. Our study therefore indicates that patches do accumulate individuals and species in a manner consistent with stochastic expectations, however, this applies primarily to the habitat generalists (unrestricted species). By the same token, increased habitat specialization by some species imposes constraints on the stochastic model such that it eventually fails.     

Development of fish communities in lakes after biomanipulation

Biomanipulation measures in the Netherlands are usually a combination of a drastic fish stock reduction and an introduction of pike fingerlings. In three small shallow lakes (Noorddiep, Bleiswijkse Zoom and Zwemlust) these measures resulted in a clear water state and the development of macrophytes. After the measures the fish community developed differently because of the new physical and biological conditions. Results of lake Noorddiep and lake Bleiswijkse Zoom showed that the fish community became more divers. Bream and carp became less dominant and were partly replaced by roach and perch. The importance of the main predator pike-perch was strongly reduced and replaced by pike and perch. The share of piscivorous fish in the total fish stock increased at all sites. The recruitment of young-of-the-year was similar or even higher in the clear overgrown areas than in the turbid water before the measures, but the recruitment of young-of-the-year to older fish differed between the species. Predation by pike and perch could not control the young-of-the-year cyprinids, but their predation may have contributed to the shift from bream to roach, because of selective predation on bream in the open water, while roach was hiding in the vegetation. The macrophytes provide new refugia and feeding conditions that favour roach and perch, but offer relatively poor survival conditions for bream and carp.     

Floral evolution and male reproductive success: Optimal dispensing schedules for pollen dispersal by animal-pollinated plants

Summary Selection favouring an outcrossing plant's ability to sire seeds generally promotes floral characters that increase (1) the frequency of pollinator visits, (2) the number of pollen grains dispersed to other plants by each pollinator and (3) the probability of a pollen grain successfully fertilizing an ovule after reaching a stigma. Flowers influence pollen dispersal and fertilization probabilities by determining the pattern of pollen removal during a series of visits (dispensing schedule). We model male reproductive success to identify optimal dispensing schedules, which characteristically involve monotonic increases in the proportion of remaining pollen removed during successive visits. These schedules balance the benefits of restricted removal, which counteracts the diminishing returns associated with animal pollination (e.g. pollinator grooming, local mate competition), with the advantages of increased removal to avoid time-dependent losses in fertilization ability (e.g. pollen precedence, declining viability). Because pollinator availability mediates this balance, the most effective dispensing schedule allows dynamic adjustment of removal to the prevailing frequency of visits experienced by individual plants. As an example of such dynamic removal we demonstrate that the dispensing mechanism ofLupinus sericeus flowers allows facultative adjustment of removal to the interval between visits. Because optimal control of pollen removal can increase a plant's mating opportunities by an order of magnitude, dispensing mechanisms should be a common component of floral design.     

Simultaneous high-biomass protein production and nutrient removal using Spirulina maxima in sea water supplemented with anaerobic effluents

Maximum protein accumulation (71%, w/w) and nutrient removal by a mutant strain of Spirulina maxima growing on sea water supplemented with anaerobically treated pig slurry was achieved at 30°C with constant illumination (60 to 70 Em^-2s^-1), using a flow rate of 14.5 cm s^-1 (20 rev. min^-1 of a paddle wheel). Total phosphates were decreased by 99% and all ammonia-N was removed under these conditions.The authors are with the Department of Environmental Biotechnology, Institute of Ecology, Aptd Postal 63, Xalapa, Ver., Mexico     

Annual survival rate and age structure of habu,Trimeresurus flavoviridis (Viperidae), on Minna island,Japan: Estimation from removal trapping

A population of a viperid snake,Trimeresurus flavoviridis, was studied over 10 years by removal trapping on a small subtropical island in Japan. The sex ratio of trapped individuals changed seasonally, but was not biased to either sex in the whole sample of 258 individuals. The age of each individual was estimated through the size structure and the age-size relationship. The minimum number of individuals at the beginning of the study was estimated through accumulating older individuals trapped in the subsequent years. By assuming an annual natural survival rate in the course of this accumulation, an age structure was simulated which led to calculate a resulted natural survival rate. The assumed rate of 0.62 fitted best to the resulted one. The annual trapped proportion estimated on the simulated absolute number of individuals was higher in older individuals than in younger ones with the overall mean of 16%.     

Nutrient-split feeding strategy for dialysis cultivation of Escherichia coli

Reduction in nutrient loss during dialysis cultivation of Escherichia coli on a glycerol medium was investigated. A dialysis reactor with an inner fermentation and an outer dialysis chamber was used. Aerobic condition was maintained by limiting the glycerol feed rate to an optimum value which was estimated from the oxygen requirements for glycerol oxidation and oxygen transfer capacity of the reactor. High reduction in nutrient loss was achieved by using water as the dialyzing fluid. However, osmotic movement of water from the dialysis to the fermentation chamber was observed, and the final cell concentration was low. With a nutrient-split feeding strategy (feeding glycerol directly to the fermentation chamber and dialyzing with salt solution), glycerol loss was small, there was no osmotic flux of water to the fermentation chamber, and the cell concentration was high. Both glycerol and salt loss could be avoided, and a cell concentration of 170 g/L was obtained when the dialysis process was substituted by addition of XAD adsorbents to the dialysis chamber. Application of this nutrient-split feeding strategy to cell cultivation in a stirred tank reactor, coupled with dialysis in external dialyzer modules, resulted in low cell concentrations. (c) 1993 Wiley & Sons, Inc.     

Short-term effects of a large dam decommissioning on biofilm structure and functioning

Aging dams and the rising efforts to restore stream ecosystems are increasing the number of dam decommissioning programs. Although dam decommissioning aims at improving in-stream habitat, biodiversity, and ecosystem functioning in the long term, it might also cause ecological impacts in the short term due to the mobilization of the sediment accumulated in the reservoir. Benthic biofilm in particular can be impaired by episodes of high turbidity and scouring. We conducted a multiple before-after/control-impact experiment to assess the effects of the drawdown of a large dam (42 m tall), a first step to its decommissioning, on biofilm structure (biomass and chlorophyll-a) and functioning (metabolism, nutrient uptake, and organic matter breakdown). Our results show that the reservoir drawdown reduced the autotrophic biofilm biomass (chlorophyll-a) downstream from the dam, which in turn lowered metabolism. However, nitrogen and phosphorus uptake by the biofilm was not affected. Organic matter breakdown was slower below the dam than in nearby undammed reaches before and during drawdown. All drawdown effects quickly disappeared and reaches downstream from the dam approached values found in nearby undammed reaches. Thus, our results indicate that the effects of reservoir drawdown on stream biofilms exist but may be small and disappear rapidly.     

好氧反硝化细菌及其在微污染水源水修复中的应用研究进展

相比于氨氮,天然水体中的硝酸盐氮通常更稳定,导致更难将其从水中去除。由于好氧反硝化可以在有氧环境下进行反硝化作用去除硝酸盐氮,该过程对含有较高溶解氧的天然水体中硝酸盐氮处理有重要作用。本文综述了好氧反硝化菌的分离纯化现状、微生物代谢机制和环境影响因子,并介绍了功能菌群在微污染饮用水源水生物修复的应用研究进展。与一般的厌氧反硝化类似,好氧反硝化菌的种属分布较广,常见的如假单胞菌属(Pseudomoas)、产碱杆菌属(Alcaligenes)、副球菌属(Paracoccus)和芽孢杆菌属(Bacillus)等所属部分微生物均有好氧反硝化能力。大部分好氧反硝化菌株在最佳生长条件下(25–37℃、溶解氧浓度为3–5mg/L、pH为7–8、碳氮比为5–10)具有高效的脱氮效率。但目前好氧反硝化作用在微污染饮用水源水的生物修复方面的应用仍有着脱氮性能不稳定、菌剂流失等不足。此外,目前较少相关中试及实际工程应用的研究,需要进一步的深入探究。     

切除上胚轴对绿豆子叶衰老逆转及其核酸和蛋白质代谢的效应

在绿豆子叶衰老达到不归点(萌发后5～6d)前切除上胚轴可使开始衰老的子叶中核酸和蛋白质含量回升,衰老短期逆转。衰老不归点后的子叶中核酸和蛋白质变化的主要特征是:丧失了较多的核主带DNA、25S、18S rRNA以及大部分可溶性蛋白质组分,一种小分子DNA 组分完全消失。不归点前切除上胚轴可使上述核酸和蛋白质组分明显增加,表明子叶衰老的逆转可能与这些重要功能物质的回升有关。在切除上胚轴的茎顶涂抹IAA,能阻止子叶核酸和蛋白质回升,也消除了切除上胚轴对子叶裹老的逆转作用。     

An automated method for modeling proteins on known templates using distance geometry.

We present an automated method incorporated into a software package, FOLDER, to fold a protein sequence on a given three-dimensional (3D) template. Starting with the sequence alignment of a family of homologous proteins, tertiary structures are modeled using the known 3D structure of one member of the family as a template. Homologous interatomic distances from the template are used as constraints. For nonhomologous regions in the model protein, the lower and the upper bounds for the interatomic distances are imposed by steric constraints and the globular dimensions of the template, respectively. Distance geometry is used to embed an ensemble of structures consistent with these distance bounds. Structures are selected from this ensemble based on minimal distance error criteria, after a penalty function optimization step. These structures are then refined using energy optimization methods. The method is tested by simulating the alpha-chain of horse hemoglobin using the alpha-chain of human hemoglobin as the template and by comparing the generated models with the crystal structure of the alpha-chain of horse hemoglobin. We also test the packing efficiency of this method by reconstructing the atomic positions of the interior side chains beyond C beta atoms of a protein domain from a known 3D structure. In both test cases, models retain the template constraints and any additionally imposed constraints while the packing of the interior residues is optimized with no short contacts or bond deformations. To demonstrate the use of this method in simulating structures of proteins with nonhomologous disulfides, we construct a model of murine interleukin (IL)-4 using the NMR structure of human IL-4 as the template. The resulting geometry of the nonhomologous disulfide in the model structure for murine IL-4 is consistent with standard disulfide geometry.