Scaling from individuals to networks in food webs

1.  Food webs, the set of predator–prey interactions in an ecosystem, are a prototypical complex system. Much research to date has concentrated on the use of models to identify and explain the key structural features which characterize food webs.
2.  These models often fall into two general categories: (i) phenomenological models which are built upon a set of heuristic rules in order to explain some empirical observation and (ii) population-level models in which interactions between individuals result in emergent properties for the food web. Both types of models have helped to uncover how food-web structure is a product of factors such as foraging behaviour, prey selection and species' body sizes.
3.  Historically, the two types of models have followed rather different approaches to the problem. Despite the apparent differences, the overlap between the two styles of models is substantial. Examples are highlighted here.
4.  By paying greater attention to both the similarities and differences between the two, we will be better able to demonstrate the ecological insights offered by phenomenological models. This will help us, for example, design experiments which could validate or refute underlying assumptions of the models. By linking models to data, scaling from individuals to networks, we will be closer to understanding the true origins of food-web structure.     

Factors controlling planktonic size spectral responses to autumnal circulation in a Mediterranean lake

1. Studies of planktonic size spectra have been common in recent years, but few concerning the effects of autumnal lake processes on those distributions have been reported. We carried out such a study for 93 days during early circulation in a small, mesotrophic, seepage lake with only benthivorous fish. Two distinct mixing periods occurred before full circulation in Las Madres lake (Spain). As a proxy of overall planktonic‐ and phytoplanktonic size distributions, the shape of a Pareto I power function was traced over time. The phytoplanktonic size spectrum was also used to test the hypothesis that phytoplankton might show a trophic cascade during early circulation. 2. Our results demonstrated that the overall size spectrum changed smoothly during the autumnal mixing, with sequential changes controlled by a combination of biotic and abiotic variables, albeit experiencing different temporal delays, always shorter than a week. A first combined, autogenic process, driven both by algal competition and a crustacean trophic effect, and a second physical‐forcing process, driven by the combined effect of convective cooling and decreasing irradiance on mixed layer dynamics, may be related to the overall planktonic spectrum in the first and second periods of mixing, respectively. 3. The phytoplanktonic size spectrum did not appear to be dictated by a trophic cascade in Las Madres lake, their dynamics being mostly controlled by physical forcing, along with some effect of non‐edible primary producers and cladocerans in the first and second periods of mixing, respectively. 4. Our results and others covering early circulation with longer sampling periods suggest that planktonic size spectral dynamics during lake circulation is context‐dependent (i.e. varying from one lake to another), thus preventing generalisation. However, when further studies with finer temporal resolution have been carried out, it is likely that clear‐cut patterns in the planktonic size spectrum will emerge, arising from the interplay of autogenic plankton dynamics, implying some resistance to community change because of external physical forcing, and the velocity of autumnal mixing.     

A Bayesian Approach to Inferring the Phylogenetic Structure of Communities from Metagenomic Data

Metagenomics provides a powerful new tool set for investigating evolutionary interactions with the environment. However, an absence of model-based statistical methods means that researchers are often not able to make full use of this complex information. We present a Bayesian method for inferring the phylogenetic relationship among related organisms found within metagenomic samples. Our approach exploits variation in the frequency of taxa among samples to simultaneously infer each lineage haplotype, the phylogenetic tree connecting them, and their frequency within each sample. Applications of the algorithm to simulated data show that our method can recover a substantial fraction of the phylogenetic structure even in the presence of high rates of migration among sample sites. We provide examples of the method applied to data from green sulfur bacteria recovered from an Antarctic lake, plastids from mixed Plasmodium falciparum infections, and virulent Neisseria meningitidis samples.     

Do Chinese cavefish show intraspecific variability in morphological traits?

Cavefishes represent one of the most bizarre and intriguing life forms inhabiting groundwater environments. One‐third of the known cavefishes worldwide is endemic to China, and almost half of those belongs to a single genus, Sinocyclocheilus (Cypriniformes: Cyprinidae). Analyzing the morphometrics of three Sinocyclocheilus species, we aimed to assess whether variability among conspecific populations exists. We predict that populations inhabiting different subterranean habitats (shallow vs. deep) show divergences in specific morphological traits to better cope with the local ecological conditions. Our results showed that the populations showing bigger eyes and reduced humpback were those occurring close to the cave entrance (habitats with light and high food availability), while specimens with smaller eyes and increased humpback were collected from deeper groundwater areas (habitats laying in darkness with food scarcity). This explorative study paves the way for further researches aiming to collect novel data on Chinese cavefishes and highlights the usefulness of these species in evolutionary studies.     

Comparative and Experimental Approaches to the Study of Microbial Food Webs

ABSTRACT The study of microbial food webs is dominated by field measurements of microbial standing stocks and rate processes and to a lesser extent by laboratory studies. These approaches reflect the concerns of microbial ecologists to assess accurately the capabilities of microorganisms and to compare microbial processes to other ecosystem parameters. These approaches have led to enormous advances in understanding microbial food webs. Reconciling our expanding knowledge with general questions about the significance and representation of microbial food webs in ecosystem studies requires additional approaches including comparative studies and field experiments. Comparative studies, analyses of microbial stocks or rates across a wide range of ecosystems, lead to quantitative models of microbial processes. These models facilitate testing of hypotheses at a very general level, allow the comparison of different stocks or rate processes across a gradient of systems, and detect unusual situations or outlier systems. Field experimental manipulations offer the advantages of working with intact natural communities, of direct evaluation of results with statistical methods, and of testing important qualitative hypotheses. Both comparative and field manipulation studies have led to important advances in the study of microbial food webs and should be expanded.     

The effects of mixotrophy on the stability and dynamics of a simple planktonic food web model

Recognition of the microbial loop as an important part of aquatic ecosystems disrupted the notion of simple linear food chains. However, current research suggests that even the microbial loop paradigm is a gross simplification of microbial interactions due to the presence of mixotrophs-organisms that both photosynthesize and graze. We present a simple food web model with four trophic species, three of them arranged in a food chain (nutrients-autotrophs-herbivores) and the fourth as a mixotroph with links to both the nutrients and the autotrophs. This model is used to study the general implications of inclusion of the mixotrophic link in microbial food webs and the specific predictions for a parameterization that describes open ocean mixed layer plankton dynamics. The analysis indicates that the system parameters reside in a region of the parameter space where the dynamics converge to a stable equilibrium rather than displaying periodic or chaotic solutions. However, convergence requires weeks to months, suggesting that the system would never reach equilibrium in the ocean due to alteration of the physical forcing regime. Most importantly, the mixotrophic grazing link seems to stabilize the system in this region of the parameter space, particularly when nutrient recycling feedback loops are included.     

Effects of Multi-chain Omnivory on the Strength of Trophic Control in Lakes

Omnivory has been implicated in both diffusing and intensifying the effects of consumer control in food chains. Some have postulated that the strong, community level, top-down control apparent in lakes is not expressed in terrestrial systems because terrestrial food webs are reticulate, with high degrees of omnivory and diverse plant communities. In contrast, lake food webs are depicted as simple linear chains based on phytoplankton-derived energy. Here, we explore the dynamic implications of recent evidence showing that attached algal (periphyton) carbon contributes substantially to lake primary and secondary productivity, including fish production. Periphyton production represents a cryptic energy source in oligotrophic and mesotrophic lakes that is overlooked by previous theoretical treatment of trophic control in lakes. Literature data demonstrate that many fish are multi-chain omnivores, exploiting food chains based on both littoral and pelagic primary producers. Using consumer-resource models, we examine how multiple food chains affect fourth-level trophic control across nutrient gradients in lakes. The models predict that the stabilizing effects of linked food chains are strongest in lakes where both phytoplankton and periphyton contribute substantially to production of higher trophic levels. This stabilization enables a strong and persistent top down control on the pelagic food chain in mesotrophic lakes. The extension of classical trophic cascade theory to incorporate more complex food web structures driven by multi-chain predators provides a conceptual framework for analysis of reticulate food webs in ecosystems.     

高通量测序技术在食品微生物研究中的应用

高通量测序技术的快速发展对食品微生物发酵过程和机制研究产生了深刻的影响,主要体现在食品微生物生理功能、代谢能力和进化的研究以及食品微生物群落结构、动态变化及其对环境的响应机制等方面。另外,通过对食品微生物基因组和元基因组进行数据分析,也对食品发酵过程优化、微生物功能改造、食源性微生物疾病预防和控制等提供了重要的依据。本文总结了近年来利用高通量测序技术对食品微生物基因组和元基因组进行测序的研究,并探讨了测序技术的发展对食品微生物研究的影响及发展趋势。     

Modeling climate change impacts on overwintering bald eagles

Bald eagles (Haliaeetus leucocephalus) are recovering from severe population declines, and are exerting pressure on food resources in some areas. Thousands of bald eagles overwinter near Puget Sound, primarily to feed on chum salmon (Oncorhynchus keta) carcasses. We used modeling techniques to examine how anticipated climate changes will affect energetic demands of overwintering bald eagles. We applied a regional downscaling method to two global climate change models to obtain hourly temperature, precipitation, wind, and longwave radiation estimates at the mouths of three Puget Sound tributaries (the Skagit, Hamma Hamma, and Nisqually rivers) in two decades, the 1970s and the 2050s. Climate data were used to drive bald eagle bioenergetics models from December to February for each river, year, and decade. Bald eagle bioenergetics were insensitive to climate change: despite warmer winters in the 2050s, particularly near the Nisqually River, bald eagle food requirements declined only slightly (<1%). However, the warming climate caused salmon carcasses to decompose more rapidly, resulting in 11% to 14% less annual carcass biomass available to eagles in the 2050s. That estimate is likely conservative, as it does not account for decreased availability of carcasses due to anticipated increases in winter stream flow. Future climate-driven declines in winter food availability, coupled with a growing bald eagle population, may force eagles to seek alternate prey in the Puget Sound area or in more remote ecosystems.     

Sulphur stable isotopes can distinguish trophic dependence on sediments and plankton in boreal lakes

1. Stable isotopes of carbon are useful for differentiating between freshwater food chains based on planktonic algae or benthic algae, but are reported to be of limited use for identifying food chains based on sedimentary detritus. Because data from marine systems suggest that stable isotopes of sulphur (δ³⁴S values) have potential in this regard, we tested their utility in freshwater lakes.
2. We found that sulphate in the water column of four boreal lakes was enriched in ³⁴S compared to the sulphur in bulk sediments from these lakes. Furthermore, within a given lake, insects known to feed on sediment (directly or via predation) had δ³⁴S values similar to those of sediment, whereas planktonic and benthic invertebrates known to feed on suspended particles had δ³⁴S values similar to those of sulphate in the water column.
3. Using the stable S isotope values of invertebrates that obtain their S from either the sediment or the water column as end members in a two-source mixing model, we show that two fish species obtain their food from both planktonic and sedimentary sources. Furthermore, model results suggest that, as expected, the more benthic-feeding fish species obtains more of its S from the sediment compartment than does the species that feeds in the water-column.
4. Our results suggest that measurements of stable sulphur isotopes provide a means of distinguishing between members of food chains that are based in the water column from those based on sedimentary detritus. As such, they would be a useful complement to stable C isotopes that are used to distinguish between food chains based on planktonic or benthic algae.     

基于稳定氧同位素确定植物水分来源不同方法的比较

利用稳定同位素技术确定植物水分来源,对提高生态水文过程的认识和对干旱半干旱区的生态管理至关重要。目前基于稳定同位素技术确定植物水分来源的方法众多,但不同方法之间对比的研究较少。本研究基于原位样品采集,室内实验测试,利用直接对比法、多元线性混合模型(IsoSource)、贝叶斯混合模型(MixSIR、MixSIAR)和吸水深度模型分析植物水分来源,并对比各方法的优缺点。结果表明:相对于多元线性混合模型(IsoSource)而言,贝叶斯混合模型(MixSIR、MixSIAR)具有更好的水源区分性能,但对数据要求较高,且植物木质部水和潜在水源同位素组成的标准差越小,模型运行结果的可信度更高。本研究中贝叶斯混合模型(MixSIR)为最优解。在利用稳定氢氧同位素技术确定植物水分来源时,可先通过直接对比法定性判断植物可能利用的潜在水源,然后再用多元线性混合模型(IsoSource)、贝叶斯混合模型(MixSIR、MixSIAR)计算出各潜在水源对植物的贡献率和贡献范围,必要时可评估模型性能,选择出最优模型,定量分析植物的水分来源。若植物主要吸收利用不同土层深度的土壤水,可结合吸水深度模型计算出植物...