Ecosystem engineering as an energy transfer process: a simple agent-based model

Ecosystem engineers are defined as organisms who modulate the availability of resources for themselves and other organisms by physically changing the environment. Ecosystem engineering is a well-recognised ecological interaction, but there is a limited number of general models due to the recent development of the field. Agent-based models are often used to study how organisms respond to changing environments and are suitable for modelling ecosystem engineering. To our knowledge, agent-based methodology has not yet been used to model ecosystem engineering. In this paper, we develop a simple agent-based population dynamics model of ecosystem engineering as an energy transfer process. We apply energy budget approach to conceptually explain how ecosystem engineers transfer energy to the environment and define various types of energy transfers relative to their effects on the engineers and other organisms. We simulate environments with various levels of resource abundance and compare the results of the model without ecosystem engineering agents to the model with ecosystem engineering agents. We find that in environments with higher levels of resources, the presence of ecosystem engineers increases the average carrying capacity and the strength of population fluctuations, while in environments with lower levels of resources, ecosystem engineering mitigates fluctuations, increases average carrying capacity and makes environments more resilient. Finally, we discuss about the further application of agent-based modelling for the theoretical and experimental development of the ecosystem engineering concept.     

A histopathological survey of shore crab (Carcinus maenas) and brown shrimp (Crangon crangon) from six estuaries in the United Kingdom

Invertebrates show considerable potential as sentinel organisms for the monitoring of the health status of aquatic systems. They are generally small, abundant, relatively sessile, and may readily bioaccumulate toxins. Cascade-like stress responses can occur following acute or chronic exposures to contaminated environments and as such, the overall health status of individuals within those environments, both in terms of histopathological lesions and the presence of infecting organisms, may ultimately reflect the general health status of these sites. The current study provides baseline multi-organ histopathological data for two common crustacean species, the shore crab (Carcinus maenas) and the brown shrimp (Crangon crangon) collected from six UK estuarine sites. Changes in the metabolic condition of crustaceans from these sites (measured in terms of connective tissue storage cell status) were interpreted in relation to other health measures (including parasite load and the presence of microbial pathogens). The relative ease at which a holistic assessment of health can be made using histopathology and the suitability of these species as environmental sentinels provide support for the inclusion of crustaceans as indicators of aquatic environmental health. Studies linking disease status to burdens of industrial contamination in these environments are now required.     

Free-living amoebae isolated from water-hyacinth root (Eichhornia crassipes)

Free-living amoebae are widely distributed in aquatic environments and their hygienic, medical and ecological relationships to man are increasingly important. The purpose of this study was to isolate free-living amoebae from water-hyacinth root (Eichhornia crassipes) and the water of an urban lake in Mexico City. Five grams of wet root were seeded on non-nutritive agar with Enterobacter aerogenes (NNE). Water samples were concentrated by centrifugation at 1200g for 15 min and the pellet was seeded on NNE. Of the 16 isolated genera, 10 were detected in both habitats. The most frequent were Vannella in root and Acanthamoeba and Naegleria in water. The total number of isolates and genera isolated from root was higher than that isolated from water. The differences between root and water are probably due to the morphological characteristics of water-hyacinth root, which provides a large habitat and refuge area for many organisms.     

The distribution of 0-group flatfish in relation to abiotic factors on the tidal flats in the brackish Dollard (Ems Estuary, Wadden Sea)

The distribution of 0-group flatfish was investigated in 1992 in the Dollard (Ems–Dollard estuary, Wadden Sea). 0-Group plaice, flounder and sole were not evenly distributed over the sampled locations. The spatial distribution pattern of 0-group flatfish in the Dollard changed during the investigation period. In the first week of sole presence, when the mean length of sole was 24–30 mm, salinity correlated significantly with sole density. The distribution of juvenile sole larger than 40 mm total length was affected by the elevation of the location: 0-group sole was restricted to the sampled site with the lowest elevation. The distribution of 0-group plaice was related to sediment: no juvenile plaice were caught at locations with more than 10% mud fraction in the sediment. The distribution of 0-group flounder was also correlated with sediment. Later in the year, salinity correlated negatively with the distribution of 0-group flounder. The influence of sediment composition is probably indirect and linked to the abundance of preferred food items, such as Corophium volutator . Abiotic conditions were suitable to 0-group plaice, flounder and sole.     

Behavioral Plasticity in Response to Environmental Manipulation among Zebrafish (Danio rerio) Populations

Plastic responses can have adaptive significance for organisms occurring in unpredictable environments, migratory species and organisms occupying novel environments. Zebrafish (Danio rerio) occur in a wide range of habitats and environments that fluctuate frequently across seasons and habitats. We expect wild populations of fish to be behaviorally more flexible than fish reared in conventional laboratory and hatchery environments. We measured three behavioral traits among 2 wild (U and PN) and 1 laboratory bred (SH) zebrafish populations in four environments differing in water flow and vegetation regimes. We found that the degree of plasticity varied with the type of behavior and also among populations. In general, vegetation increased aggression and water flow decreased latency to feed after a disturbance, but the patterns were population dependent. For example, while wild U fish fed more readily after a disturbance in vegetated and/or flowing habitats, fish from the wild PN population and lab-reared SH strain showed little variation in foraging across different environmental conditions. Zebrafish from all the three populations were more aggressive when tested in an arena with vegetation. In contrast, while there was an inter- population difference in shoaling distances, variation in shoaling distance across environmental conditions within populations was not significant. These results suggest that both foraging and aggression in zebrafish are more plastic and influenced by immediate context than is shoaling distance, which may have a stronger genetic basis. Our findings point to different underlying mechanisms influencing the expression of these traits and warrants further investigations.     

The ecological effect of phenotypic plasticity — Analyzing complex interaction networks (COIN) with agent-based models

Analyzing complex dynamics of ecological systems is complicated by two important facts: First, phenotypic plasticity allows individual organisms to adapt their reaction norms in terms of morphology, anatomy, physiology and behavior to changing local environmental conditions and trophic relationships. Secondly, individual reactions and ecological dynamics are often determined by indirect interactions through reaction chains and networks involving feedback processes.

We present an agent-based modeling framework which allows to represent and analyze ecological systems that include phenotypic changes in individual performances and indirect interactions within heterogeneous and temporal changing environments. We denote this structure of interacting components as COmplex Interaction Network (COIN).

Three examples illustrate the potential of the system to analyze complex ecological processes that incorporate changing phenotypes on the individual level:

• A model on fish population dynamics of roach (Rutilus rutilus) leads to a differentiation in fish length resulting in a conspicuous distribution that influences reproduction capability and thus indirectly the fitness.

• Modeling the reproduction phase of the passerine bird Erithacus rubecula (European Robin) illustrates variation in the behavior of higher organisms in dependence of environmental factors. Changes in reproduction success and in the proportion of different activities are the results.

• The morphological reaction of plants to changes in fundamental environmental parameters is illustrated by the black alder (Alnus glutinosa) model. Specification of physiological processes and the interaction structure on the level of modules allow to represent the reaction to changes in irradiance and temperature accurately.

Applying the COIN-approach, individual plasticity emerges as a structural and functional implication in a self-organized manner. The examples illustrate the potential to integrate existing approaches to represent detailed and complex traits for higher order organisms and to combine ecological and evolutionary aspects.

桃儿七分布格局与生态适应的初步研究

以云南产桃儿七Ｓｉｎｏｐｏｄｏｐｈｙｌｌｕｍ ｈｅｘａｎｄｒｕｍ（Ｒｏｙｌｅ）Ｙｉｎｇ为研究材料,分析了它的分布格局及生态适应。指出桃儿七是一个分布范围较广、生态适应幅度大的物种;在分布区内它主要出现在具有次生植被的山谷中,个体在居群内的分布格局,由于受到放牧活动的影响而呈聚群式分布,植株常出现在灌木丛下和树根附近。它适应夏秋湿润凉爽,冬季及早春寒冷干燥的气候条件,并具有相应的生长与发育节律。人类     

机会（r—选择）和均衡（Ｋ—选择）遗迹化石的现代生态学解释

介绍地质记录中在不稳定的沉环境下,由于生活条件的恶化（盐度的变,严酷的温度,低含氧量及移动的沉积基底等）以及沉积事件（浊流沉积和风暴沉积）所产生的机会(r-选择）遗迹化石和均衡（Ｋ－选择）遗迹化石及其特点以及机会行为方式的古生物证据。对现代底栖生物的生态学研究,揭示现代机会生物均衡生物的生态特征（居群策略）描述由于破坏事件导致动物群消除后重新移居的现代实例,有助于了解地质记录中机会(r-选择）遗迹化石和均衡（Ｋ－选择）遗迹化石的成因及其古生态特征。     

生态基因组学研究进展

生态基因组学是一个整合生态学、分子遗传学和进化基因组学的新兴交叉学科。生态基因组学将基因组学的研究手段和方法引入生态学领域,通过将群体基因组学、转录组学、蛋白质组学等手段与方法将个体、种群及群落、生态系统不同层次的生态学相互作用整合起来,确定在生态学响应及相互作用中具有重要意义的关键的基因和遗传途径,阐明这些基因及遗传途径变异的程度及其生态和进化后果的特征,从基因水平探索有机体响应天然环境(包括生物与非生物的环境因子)的遗传学机制。生态基因组学的研究对象可以分为模式生物与非模式生物两大类。拟南芥、酿酒酵母等模式生物在生态基因组学领域发挥了重要作用。随着越来越多基因组学技术的开发与完善,越来越多的非模式生物生态基因组学的研究将为生态学的发展提供重要的理论与实践依据。生态基因组学最核心的方法包括寻找序列变异、研究基因差异表达和分析基因功能等方法。生态基因组学已广泛渗透到生态学的相关领域中,将会在生物对环境的响应、物种间的相互作用、进化生态学、全球变化生态学、入侵生态学、群落生态学等研究领域发挥更大的作用。     

A needle in a haystack: A new metabarcoding approach to survey diversity at the species level of Arcellinida (Amoebozoa: Tubulinea)

Environmental DNA-based diversity studies have increased in popularity with the development of high throughput sequencing technologies. This permits the potential simultaneous retrieval of vast amounts of molecular data from many different organisms and species, thus contributing to a wide range of biological disciplines. Environmental DNA protocols designed for protists often focused on the highly conserved small subunit of the ribosome gene, that does not permit species-level assignments. On the other hand, eDNA protocols aiming at species-level assignments allow a fine level ecological resolution and reproducible results. These protocols are currently applied to organisms living in marine and shallow lotic freshwater ecosystems, often in a bioindication purpose. Therefore, in this study, we present a species-level eDNA protocol designed to explore diversity of Arcellinida (Amoebozoa: Tubulinea) testate amoebae taxa that is based on mitochondrial cytochrome oxidase subunit I (COI). These organisms are widespread in lentic water bodies and soil ecosystems. We applied this protocol to 42 samples from peatlands, estuaries and soil environments, recovering all the infraorders in Glutinoconcha (with COI data), except for Hyalospheniformes. Our results revealed an unsuspected diversity in morphologically homogeneous groups such as Cylindrothecina, Excentrostoma or Sphaerothecina. With this protocol we expect to revolutionize the design of modern distributional Arcellinida surveys. Our approach involves a rapid and cost-effective analysis of testate amoeba diversity living in contrasted ecosystems. Therefore, the order Arcellinida has the potential to be established as a model group for a wide range of theoretical and applied studies.     

Experimental demonstration of accelerated extinction in source‐sink metapopulations

Population extinction is a fundamental ecological process which may be aggravated by the exchange of organisms between productive (source) and unproductive (sink) habitat patches. The extent to which such source‐sink exchange affects extinction rates is unknown. We conducted an experiment in which metapopulation effects could be distinguished from source‐sink effects in laboratory populations of Daphnia magna. Time‐to‐extinction in this experiment was maximized at intermediate levels of habitat fragmentation, which is consistent with a minority of theoretical models. These results provided a baseline for comparison with experimental treatments designed to detect effects of concentrating resources in source patches. These treatments showed that source‐sink configurations increased population variability (the coefficient of variation in abundance) and extinction hazard compared with homogeneous environments. These results suggest that where environments are spatially heterogeneous, accurate assessments of extinction risk will require understanding the exchange of organisms among population sources and sinks. Such heterogeneity may be the norm rather than the exception because of both the intrinsic heterogeneity naturally exhibited by ecosystems and increasing habitat fragmentation by human activity.     

Response of common seals (Phoca vitulina) to human disturbances in the Dollard estuary of the Wadden Sea

The Dollard area is a core breeding area of common seals, Phoca vitulina, in the Dutch Wadden Sea. Seals mainly use this area in the birth season, and it is at this time that mother and pup pairs are prone to disturbance. Seals in the Dollard lie on sandbanks close to the dyke area which exposes them to various human activities on land and in the coastal waters.The colony of common seals on the sandbanks of the Dollard has increased from 77 individuals in 1993 to 332 in 2010. Observations were made during the pupping and lactation seasons in 2007, 2008, 2009 and 2010. In total, 692 h of observations were made over the last 4 years, and a total of 1329 potential disturbances were recorded. Human activities were more frequent on land than on water or in the air. In total, most disturbances were also recorded as arising from land. Actual disturbances of seals were recorded 344 times; seals were alerted 249 times and seals escaped into the water 95 times. An escape response was observed for 81 of the 1037 (7.8%) recorded land activities, 6 of the 92 (6.5%) recorded water activities, and 8 of the 200 (4%) air activities. These percentages of escape responses did not differ significantly between the land, water and air activities.The construction of a culvert in the dyke in 2001, and the building up of sand ridges along the water flow towards the culvert, provided the seals with an extra place to haul out. Land activities only affected seals resting on these sand ridges which are at a distance of 50–200 m of the dyke. Boats have the potential to disturb seals on all sandbanks of the study area. They affected the highest number of seals per disturbance, with up to 117 animals fleeing into the water. Flying at lower altitudes appeared to cause more disturbances of seals. Therefore, the effect of flying at low altitudes (150–300 m) warrants further investigation.Disturbances which lead to fleeing into the water create the potential risk of separating pups from their mothers. This may contribute to the high incidence of orphaned pups found in the Dollard region. Yearly numbers fluctuated between 13 and 24 orphans representing a substantial proportion of the seals born in this area (with highest pup counts of ca. 100). In addition to separation, disturbances may also impact the condition of pups if they occur repeatedly during suckling.The results of this study demonstrate that disturbance is caused by various human activities to a colony of seals using sandbanks close to the mainland. As these disturbances pose a risk that pups become orphaned or are impacted in terms of their body condition, efforts should be made to minimise the effects of human presence.     

Influence of salinity on the rates of oxygen consumption in two species of freshwater fishes,Phoxinus erythrogaster (family Cyprinidae), and Fundulus catenatus (family Fundulidae)

A dye process in a textile plant in southern Kentucky (USA) produces large quantities of saline waste-water which eventually enter Lake Cumberland via a municipal sewage treatment plant on Lily Creek. The impact of hypersaline conditions on two fish species native to the Cumberland River drainage system, redbelly dace (Phoxinus erythrogaster) and northern studfish (Fundulus catenatus), was assessed. These species were subjected to salinities of 0, 4, and 10 after which routine oxygen consumtpion values were determined. Significant correlations of salinity with oxygen consumption were demonstrated for both species with P. erythrogaster showing greater overall impact of salinity on metabolic rate.     

Social flexibility and social evolution in mammals: a case study of the African striped mouse (Rhabdomys pumilio)

Environmental change poses challenges to many organisms. The resilience of a species to such change depends on its ability to respond adaptively. Social flexibility is such an adaptive response, whereby individuals of both sexes change their reproductive tactics facultatively in response to fluctuating environmental conditions, leading to changes in the social system. Social flexibility focuses on individual flexibility, and provides a unique opportunity to study both the ultimate and proximate causes of sociality by comparing between solitary and group-living individuals of the same population: why do animals form groups and how is group-living regulated by the environment and the neuro-endocrine system? These key questions have been studied for the past ten years in the striped mouse Rhabdomys pumilio. High population density favours philopatry and group-living, while reproductive competition favours dispersal and solitary-living. Studies of genetic parentage reveal that relative fitness of alternative reproductive tactics depends on the prevailing environment. Tactics have different fitness under constrained ecological conditions, when competitive ability is important. Under conditions with relaxed ecological constraints, alternative tactics can yield equal fitness. Both male and female striped mice display alternative reproductive tactics based on a single strategy, i.e. all individuals follow the same decision rules. These changes are regulated by endocrine mechanisms. Social flexibility is regarded as an adaptation to unpredictably changing environments, selecting for high phenotypic flexibility based on a broad reaction norm, not on genetic polymorphism for specific tactics.     

Reductive precipitation of gold by dissimilatory Fe(III)-reducing bacteria and archaea.

Studies with a diversity of hyperthermophilic and mesophilic dissimilatory Fe(III)-reducing Bacteria and Archaea demonstrated that some of these organisms are capable of precipitating gold by reducing Au(III) to Au(0) with hydrogen as the electron donor. These studies suggest that models for the formation of gold deposits in both hydrothermal and cooler environments should consider the possibility that dissimilatory metal-reducing microorganisms can reductively precipitate gold from solution.     

Ecological genomics: understanding gene and genome function in the natural environment

The field of ecological genomics seeks to understand the genetic mechanisms underlying responses of organisms to their natural environments. This is being achieved through the application of functional genomic approaches to identify and characterize genes with ecological and evolutionary relevance. By its very nature, ecological genomics is an interdisciplinary field. In this review, we consider the significance of this new area of study from both an ecological and genomic perspective using examples from the recent literature. We submit that by considering more fully an ecological context, researchers may gain additional insights into the underlying genetic basis of ecologically relevant phenotypic variation. Likewise, genomic approaches are beginning to offer new insights into higher-level biological phenomena that previously occupied the realm of ecological investigation only. We discuss various approaches that are likely to be useful in ecological genomic studies and offer thoughts on where this field is headed in the future.     

Large net cage for captive breeding and behavioural studies of damselfly Lestes sponsa (Hansemann, 1823) (Odonata: Lestidae): submerged oviposition as a model behaviour

Odonata have a strong potential as model organisms for testing ecological and evolutionary hypotheses because of their short life history, relative ease and cost-effectiveness of care. Unfortunately, very few studies have examined how to create a semi-natural environment for odonates, limiting the biological validity of laboratory manipulation. To better study odonate life cycle and behaviour under controlled conditions, we designed a large net cage that imitated the natural terrestrial as well as aquatic habitat of the damselfly Lestes sponsa (Hansemann, 1823). This species is thought to be capable of submerged oviposition, an unusual behaviour in odonates. We compared multiple variables across natural conditions and the net cage. We demonstrated that between-year variability under natural conditions was generally greater than variability between natural and artificial environments. Overall, semi-natural conditions did not substantially change the L. sponsa life cycle (including the unique behaviour of submerged oviposition), suggesting that results from the net cage are likely generalisable to the field.     

Significance of palaeoberesellids (Chlorophyta) in Dinantian sedimentation, UK

Palaeoberesellids are septate, tubular microfossils usually attributed to the green algae. They occur widely in Upper Palaeozoic carbonate sediments, where they are normally seen in thin sections as cross-sections or short lengths of thallus. Detailed study of late Dinantian (Asbian) limestones from two areas of the UK. South Wales and northwest England, show that palaeoberesellids. particularly Kamaenella . are the most important carbonate-producing organisms in shallow. low to moderate energy environments and supplied grains to higher energy environments as a result of storm breakage and transport. Where palaeoberesellids were the dominant organisms they formed low-growing 'thickets' on the sea-floor which trapped fine sediment. to create a bafflestone texture. The late Dinantian was a time of great instability with rapid sea-level changes. Palaeoberesellids were opportunistic organisms which thrived in such an environment. The volume of carbonate produced by these organisms in shallow water may have been a contributory factor in the progradation of shallow marine facies and the establishment of relatively flat-topped shelves from the ramps of the Early Dinantian.     

Ontogenetic phenotypic plasticity during the reproductive phase in Arabidopsis thaliana (Brassicaceae)

While phenotypic plasticity has been the focus of much research and debate in the recent ecological and evolutionary literature, the developmental nature of the phenomenon has been mostly overlooked. A developmental perspective must ultimately be an integral part of our understanding of how organisms cope with heterogeneous environments. In this paper I use the rapid cycling Arabidopsis thaliana to address the following questions concerning developmental plasticity. (1) Are there genetic and/or environmental differences in parameters describing ontogenetic trajectories? (2) Is ontogenetic variation produced by differences in genotypes and/or environments for two crucial traits of the reproductive phase of the life cycle, stem elongation and flower production? (3) Is there ontogenetic variability for the correlation between the two characters? I found genetic variation, plasticity, and variation for plasticity affecting at least some of the growth parameters, indicating potential for evolution via heterochronic shifts in ontogenetic trajectories. Within-population differences among families are determined before the onset of the reproductive phase, while among-population variation is the result of divergence during the reproductive phase of the ontogeny. Finally, the ontogenetic profiles of character correlations are very distinct between the ecologically meaningful categories of early- and late-flowering “ecotypes” in this species, and show susceptibility to environmental change.     

Toxicity Assessment of Iron Oxide Nanoparticles in Zebrafish (Danio rerio) Early Life Stages

Iron oxide nanoparticles have been explored recently for their beneficial applications in many biomedical areas, in environmental remediation, and in various industrial applications. However, potential risks have also been identified with the release of nanoparticles into the environment. To study the ecological effects of iron oxide nanoparticles on aquatic organisms, we used early life stages of the zebrafish (Danio rerio) to examine such effects on embryonic development in this species. The results showed that ≥10 mg/L of iron oxide nanoparticles instigated developmental toxicity in these embryos, causing mortality, hatching delay, and malformation. Moreover, an early life stage test using zebrafish embryos/larvae is also discussed and recommended in this study as an effective protocol for assessing the potential toxicity of nanoparticles. This study is one of the first on developmental toxicity in fish caused by iron oxide nanoparticles in aquatic environments. The results will contribute to the current understanding of the potential ecotoxicological effects of nanoparticles and support the sustainable development of nanotechnology.