Application of biotic and taxonomic distinctness indices in assessing the Ecological Quality Status of two coastal lakes: Caprolace and Fogliano lakes (Central Italy)

Marine biotic indices (AMBI, BENTIX) and the statistical tool M-AMBI (Multivariate AMBI) were applied as a comparative approach in assessing the Ecological Quality Status (EcoQS) of two Mediterranean coastal lakes (Caprolace and Fogliano lakes) situated in the Circeo National Park (Central Italy). The macrobenthic community was analysed using univariate indices (community structure), correspondence analysis (CA) and taxonomic distinctness indices (Δ⁺ and Λ⁺). The community composition showed a dominance of lagoonal species in both coastal lakes, while in Caprolace lake marine taxa were also found. Diversity index (H′) complies to ranges found in Mediterranean lagoons and taxonomic distinctness indices demonstrated that taxonomy structure is in accordance with natural variability ranges. Principal component analysis (PCA) on chemical parameters of water and sediment showed that both coastal lakes differ mainly in their organic matter composition. In fact, the protein fraction of bio-polymeric carbon prevails in Fogliano lake, while the ‘refractory’ component represented by carbohydrate fraction is predominant in Caprolace lake. The difference between the two coastal lakes was also demonstrated by co-inertia analysis (COIA) performed using abundance of species and concentrations of chemical parameters. The results from the application of the three biotic indices do not highlight a clear distinction between the two lagoons. However, the AMBI index provided a more suitable evaluation of EcoQS corresponding to ‘slightly polluted’ lagoons while M-AMBI and moreover BENTIX indices indicated a worsening situation. The biotic indices are widely used in assessing the EcoQS in marine environments, but their proper application in transitional waters would depend on a resettlement; thresholds established in the biotic index scale values need to be modified according to natural variability of transitional waters referring to abiotic conditions and abundance of tolerant species.     

The derivation, performance and role of univariate and multivariate indicators of benthic change: Case studies at differing spatial scales

In Europe there is an extensive history of the derivation and use of benthic indicators which parallels similar developments in North America and elsewhere. Most recently, this has increased because major European Union Directives require that indicators of marine benthic change are used to confirm good ecological status quality (as in the Water Framework Directive) and favourable conservation status (as in the Habitats and Species Directive). Furthermore, these indicators have to fit within the current philosophy of the Ecosystem Approach requiring the development and use of Ecological Quality Objectives and Standards. Despite this, comparisons of families of indicators derived by differing methods have not been carried out such that the robust nature of the indicators on differing spatial scales and under differing benthic conditions has not been rigorously assessed. Using case studies from the Portuguese coasts and estuaries, this paper compares and contrasts univariate and multivariate macrobenthic indicators to quantify comparisons of change. The studies indicate the relative value of those indicators at contrasting spatial scales, e.g. in the transition from small areas around coastal submarine outfalls, to the local and regional estuarine and coastal scale. The analysis indicates the difficulties of deriving and using qualitative and quantitative indicators from benthic communities in stable, and in moderately and highly variable environmental conditions in estuarine, coastal and open sea habitats. In some areas, the variability in the indicators and indices within a station and site is as large as that between stations and sites. For those areas studied, there is an adequate quality and quantity of benthic data available for making management decisions but this is unlikely to be the case for all areas. Similarly, the interrogation of the methods shows that while their use and interpretation rely on a good understanding of the biology of the individual species and their responses to physical and polluting stress, that understanding is not yet available for many of the species. Most notably, while the indices and integrative indicators are becoming increasingly sophisticated, many are still dependent on the Pearson-Rosenberg model for organic enrichment hence they require to be validated for physical disturbance and for chemical pollution. Because of these features, the outcome of the analysis has repercussions for the management of coastal and estuarine areas. Although the present study indicates the value of indicators of benthic change for making management decisions at the various scales, further validation is required especially, for example, where one indicator over-estimates the ecological status for poor areas and underestimates it for good areas.     

天然活性多肽的发掘策略和生产技术

活性多肽可以参与生命机体的多种生理活动,对促进人体健康发挥着重要的作用,如降血压、降血糖、降血脂和抗癌等,其创制技术也逐渐成为重要的研究和应用转化方向。本综述旨在总结天然活性多肽的发掘策略和生产技术的研究进展。目前,天然活性多肽的发掘与生产技术主要包括自上而下和自下而上两种方法,其中自上而下方法在多肽发掘方面主要为直接提取鉴定法,在生产技术方面主要包括直接提取法、酶解法和微生物发酵法;自下而上方法在多肽发掘方面包括天然活性多肽改造和数据库发掘方法,在生产技术方面主要方法包括化学合成法、酶合成法、基因重组表达法和无细胞合成法。自上而下的天然多肽制备与功能验证方法存在步骤烦琐、耗费时间长、功能不确定性大、实验与生产成本高以及质量控制难度大等问题;而自下而上的活性多肽合成与功能验证方法适合多肽药物的开发,而难以用于功能食品。随着测序和质谱技术的发展,人们更容易从分子水平获取物种蛋白组信息。以此蛋白组信息为根据,将自上而下和自下而上两种方法结合,可以克服单独使用这两种方法存在的问题,从而为快速开发和生产天然活性多肽提供新的策略。     

Assessment of Top-Down and Bottom-Up Controls on the Collapse of Alewives (<Emphasis Type="Italic">Alosa pseudoharengus</Emphasis>) in Lake Huron

Food web models are powerful tools to inform management of lake ecosystems, where top-down (predation) and bottom-up (resource) controls likely propagate through multiple trophic levels because of strong predator–prey links. We used the Ecopath with Ecosim modeling approach to assess these controls on the Lake Huron main basin food web and the 2003 collapse of an invasive pelagic prey fish, alewife (Alosa pseudoharengus). We parameterized two Ecopath models to characterize food web changes occurring between two study periods of 1981–1985 and 1998–2002. We also built an Ecosim model and simulated food web time-dynamics under scenarios representing different levels of top-down control by Chinook salmon (Oncorhynchus tshawytscha) and of bottom-up control by quagga mussels (Dreissena rostriformis bugensis) and nutrients. Ecopath results showed an increase in the relative importance of bottom-up controls between the two periods, as production decreased across all trophic levels. The production of non-dreissenid benthos decreased most, which could cause decreases in production of pelagic prey fishes feeding on them. Ecosim simulation results indicated that the alewife collapse was caused by a combination of top-down and bottom-up controls. Results showed that while controls by Chinook salmon were relatively constant before alewife collapse, controls by quagga mussels and nutrients increased jointly to unsustainable levels. Under current conditions of low nutrients and high quagga mussel biomass, simulation results showed that recovery of alewives is unlikely regardless of Chinook salmon biomass in Lake Huron, which implies that the shrinking prey base cannot support the same level of salmonine predators as that prevailed during the 1980s.     

The management of European estuaries: A comparison of the features,controls and management framework of the Tagus (Portugal) and Humber (England)

The paper describes the local, national, European and wider-area framework, statutes, and formal and voluntary mechanisms for managing European estuaries. These aspects are discussed in relation to two large and representative estuarine systems, the Tagus, Portugal, and the Humber, on the English North Sea coast As estuaries are sites of many activities and uses, most of which are encouraged or at least condoned, management has the role of preventing and resolving conflicts between those uses and users. Accepted uses of estuaries include the discharge and dumping of waste materials, fin and shell-fisheries, conservation, land reclamation, natural usage, abstraction by industry, and recreation. Estuarine management is now being carried out within the constraints of local and regional government planning, planning and activities of water pollution control bodies, fisheries control bodies, and navigation and port authorities The Tagus and Humber estuaries support all of the above activities and uses, and have controls within a European legislative framework but have differing histories of management and planning in order to resolve conflicts. In addition the Humber is subject to controls placed on North Sea areas. The paper discusses the relevant national and European legislation (Directives) and accepted practices for management. Furthermore, the paper discusses the formulation and practice of estuarine management plans as used by various bodies (nature conservation, water quality and regional authority). It is of particular note that the lessons from these two estuaries are relevant to many other European estuaries.     

Creation of Functional Micro/Nano Systems through Top-down and Bottom-up Approaches

Mimicking nature's approach in creating devices with similar functional complexity is one of the ultimate goals of scientists and engineers. The remarkable elegance of these naturally evolved structures originates from bottom-up self-assembly processes. The seamless integration of top-down fabrication and bottom-up synthesis is the challenge for achieving intricate artificial systems. In this paper, technologies necessary for guided bottom-up assembly such as molecular manipulation, molecular binding, and the self assembling of molecules will be reviewed. In addition, the current progress of synthesizing mechanical devices through top-down and bottom-up approaches will be discussed.     

Inter-hemispheric comparison of bottom-up effects on community structure: Insights revealed using the comparative-experimental approach

The comparative-experimental approach uses identically designed, replicated experiments at different sites along environmental gradients in order to gain insight into the changing dynamics of communities with changing environmental conditions. Such studies reveal how ecological processes vary in intensity and interact to produce community structure. Early emphases were on the community consequences of shifting top-down impacts, competition and disturbance with environmental stress. Recent advances include the more precise quantification of gradients and thus a better understanding of species responses to the environment, and the revelation that bottom-up forces can vary significantly on within-region scales, with major consequences for the impact of top-down forces and thus community dynamics. Here the use of the method to examine the role of geographic location (coastal ecosystems in different hemispheres) and oceanographic conditions (upwelling vs downwelling) on these bottom-up/top-down linkages is advanced. We show that a bottom-up factor (prey recruitment) and a top-down effect (predation rate) vary consistently with oceanographic conditions within each coastal ecosystem, and also between geographic locations (New Zealand, Oregon). In general, both recruitment and predation rates are higher in Oregon. It is postulated that these differences are common responses to oceanographic variation, and that between-hemisphere differences result from the stronger and more persistent upwelling in the California Current ecosystem.     

Defining past ecological status and in situ reference conditions using benthic foraminifera: A case study from the Oslofjord,Norway

Characterizing marine water bodies and defining ecological status, both present and past (pre-impacted), has become an important task for EU's Member States and their associates during the last decade due to the implementation of the Water Framework Directive (WFD). However, none of the methods used to define Ecological Quality Status (EcoQS) are able to accurately define the status for both the present-day and reference conditions at a given site (i.e., in situ). Recent studies have revealed a significant correlation between the diversity of living (stained) fossilizable benthic foraminifera (protists) and associated environmental parameters (e.g., dissolved oxygen concentration). The present study takes this relationship a step further by applying methods used to define present-day EcoQS on fossil benthic foraminiferal assemblages and, thereby, defining past EcoQS (PaleoEcoQS). This is particularly useful for defining reference condition in areas where biological- and instrumental time-series are limited or lacking. Our case study from the Oslofjord, Norway, shows that (1) the “Foraminiferal method” can define temporal developments in in situ EcoQS from reference to present-day conditions, (2) results of the “Foraminiferal method” reflect available historical biological records and hydrographic time series, (3) data (1993 and 2009) on macrofauna (traditional bio-monitoring tool) and benthic foraminifera from the same sites define the same EcoQS, and (4) the changes in foraminiferal diversity through time are due to human activity (pollution), rather than climate change. Using in situ data to define ecological reference conditions is preferable compared to modeling or comparisons with present-day supposedly similar reference conditions.     

Ecohydrology as a new tool for sustainable management of estuaries and coastal waters

Throughout the world, estuaries and coastal waters have experienced degradation. Present proposed remedial measures based on engineering and technological fix are not likely to restore the ecological processes of a healthy, robust estuary and, as such, will not reinstate the full beneficial functions of the estuary ecosystem. The successful management of estuaries and coastal waters requires an ecohydrologybased, basin-wide approach. This necessitates changing present practices by official institutions based on municipalities or counties as an administrative unit, or the narrowly focused approaches of managers of specific activities (e.g., farming and fisheries, water resources, urban and economic developments, wetlands management and nature conservationists). Without this change in thinking and management concept, estuaries and coastal waters will continue to degrade, whatever integrated coastal management plans are implemented. To help in this process of change there is a need to (1) develop a profound understanding of the effects of biota and biotic processes on mediating estuary response to changing hydrology, sediment and nutrient flux and of the biota on hydrology at the river basin scale, and (2) to develop science-based remediation measures at the river basin scale, with elements of ecohydrology and phytotechnology at their core, to strengthen the ability of the biota to sustain and adapt to human-induced stresses.This revised version wa published online in March 2005 with corrections to the issue cover date.     

Combined effects of nutrients and grazers on bacterioplankton and phytoplankton abundance in an Antarctic lake with even food-chain links

The goal of this study was to address the top-down and bottom-up controls on different microbial web components (bacterioplankton, picophytoplankton, and >3 μm phytoplankton) in an Antarctic lake. Two experiments using a size fractionation approach and nutrient addition were conducted at microcosm scale (2.5 l). The variation in net growth rates (k′) of bacterioplankton and phytoplankton size fractions was analyzed after 5 days. The results determined significant differences; whereas bacterioplankton and large phytoplankton showed an increase in their k′ when their predators were removed, the picophytoplankton showed a decrease. All the studied plankton components presented the highest k′ when nutrients were added. It is suggested that, in this lake, both the top-down and bottom-up regulations account for the regulation of bacterioplankton and large phytoplankton. As for picophytoplankton, the bottom-up control was evident and grazing did not pose a negative impact and rather, had a positive effect probably due to liberation of nutrients.     

Modelling the influence of nutrient loads on Portuguese estuaries

The effects of implementing Directive 91/271/EEC of 21 May 1991 (Waste Water Treatment Plan Directive) and Directive 91/676/EEC of 12 December (Nitrates Directive) are analysed in 7 Portuguese estuaries (Minho, Lima, Douro, Mondego, Tagus, Sado and Guadiana) and two coastal lagoons (Ria de Aveiro and Ria Formosa), with a modelling approach. MOHID Water Modelling System was used to perform simulations with three nitrogen load scenarios for each system: a reference scenario, a 50% nitrate removal by agriculture scenario and another with a 100% nutrients removal by waste water treatment plants (WWTP). It is shown that the interaction between hydrodynamic and ecological processes is an important feature to study trophic problems in estuaries. Ecological processes such as primary production only occur inside the system if the residence time of water is high enough to enable organismal activity and if the adequate conditions are found (e.g. light, nutrients, temperature). From the model results it is possible to conclude: (i) in systems with short residence time a reduction in nutrient load will only produce a decrease in nutrient transit and will not affect the system’s global ecological status (e.g. Douro Estuary); (ii) in systems with long residence time the effects will range from significant, when primary production is mostly limited by nutrients (e.g. Ria de Aveiro), to non-significant, when primary production in the system is light-limited (e.g. Tagus Estuary).     

A periodic table for ecology? A chemist's view of plant functional types

Abstract. A functional type approach, in which the complexity found in nature is reduced by grouping organisms that are functionally similar into a single classification, is being promoted in global change research. This paper examines a proposed analogy between this functional type approach in global change ecology and the periodic table of the elements in chemistry. When applied to a ‘bottom-up’ approach for defining functional types in ecology, in which large numbers of organisms are classified into smaller groups based on similarity of certain functions, the analogy fails. Ecological functions are not simple attributes of a biological entity, as electronic structure is for a chemical element, but are themselves complex chemical and physical systems that often interact strongly with the environment. The analogy to the periodic table may be of some use as an organizing tool in a ‘top-down’ approach in which a modelling context is used to define the number of ‘elements’ and their properties. This will be elaborated for plant functional types. Each PFT is assigned characteristics that allow its response to the driving forces of change, e.g. temperature, precipitation, soil nutrients, disturbance, to be predicted. ‘Rules of combination’ determine how the mix of PFTs in a particular ecosystem changes to form different ecosystems, which would correspond in the analogy to chemical compounds. However, these requirements present significant challenges to the usefulness of the analogy, even as an organizing tool in the ‘top-down’ approach.     

Microscale methods to assemble mammalian cells into tissue-like structures

Different cell types make up tissues and organs hierarchically and communicate within a complex, three-dimensional (3D) environment. The in vitro recapitulation of tissue-like structures is meaningful, not only for fundamental cell biology research, but also for tissue engineering (TE). Currently, TE research adopts either the top-down or bottom-up approach. The top-down approach involves defining the macroscopic tissue features using biomaterial scaffolds and seeding cells into these scaffolds. Conversely, the bottom-up approach aims at crafting small tissue building blocks with precision-engineered structural and functional microscale features, using physical and/or chemical approaches. The bottom-up strategy takes advantage of the repeating structural and functional units that facilitate cell-cell interactions and cultures multiple cells together as a functional unit of tissue. In this review, we focus on currently available microscale methods that can control mammalian cells to assemble into 3D tissue-like structures.     

Marine protected area strategies: issues, divergences and the search for middle ground

There has been a dramatic increase in recentyears in the number of papers, reports, etc.,which have been published concerning MarineProtected Areas (MPAs). This overview of theobjectives, selection, design and management ofMPAs aims to provide a basis for discussionregarding possible ways forward by identifyingemerging issues, convergences and divergences. Whilst the attributes of the marine environmentmay limit the effectiveness of site-specificinitiatives such as MPAs, it is argued that itwould be defeatist in the extreme to abandonMPAs in the face of these limitations. Ten keyobjectives for MPAs are discussed, includingthat of harvest refugia, and it is argued thatwhilst these objectives may be justifiable froma preservationist perspective, they may beobjected to from a resource exploitationperspective. MPAs generate both internal(between uses) and basic (between use andconservation) conflicts, and it is argued thatthese conflicts may be exacerbated whenscientific arguments for MPAs are motivated bypreservationist concerns. It is reported thata minority of MPAs are achieving theirmanagement objectives, and that for themajority insufficient information was availablefor such effectiveness evaluations. Structureand process-oriented perspectives on marineconservation are discussed. It is argued thatthere are two divergent stances concerningoptimal MPA management approaches: top-down,characterized as being government-led andscience-based, with a greater emphasis onset-aside; and bottom-up, characterized asbeing community-based and science-guided, witha greater emphasis on multiple-use. Given thedivergent values of different stakeholders, thehigh degree of scientific uncertainty, and thehigh marine resource management decisionstakes, it is concluded that a key challenge isto adopt a ``middle-ground' approach whichcombines top-down and bottom-up approaches, andwhich is consistent with the post-normalscientific approach.     

Metabarcoding of shrimp stomach content: Harnessing a natural sampler for fish biodiversity monitoring

Given their positioning and biological productivity, estuaries have long represented key providers of ecosystem services and consequently remain under remarkable pressure from numerous forms of anthropogenic impact. The monitoring of fish communities in space and time is one of the most widespread and established approaches to assess the ecological status of estuaries and other coastal habitats, but traditional fish surveys are invasive, costly, labour intensive and highly selective. Recently, the application of metabarcoding techniques, on either sediment or aqueous environmental DNA, has rapidly gained popularity. Here, we evaluate the application of a novel, high‐throughput DNA‐based monitoring tool to assess fish diversity, based on the analysis of the gut contents of a generalist predator/scavenger, the European brown shrimp, Crangon crangon. Sediment and shrimp samples were collected from eight European estuaries, and DNA metabarcoding (using both 12S and COI markers) was carried out to infer fish assemblage composition. We detected 32 teleost species (16 and 20, for 12S and COI, respectively). Twice as many species were recovered using metabarcoding than by traditional net surveys. By comparing and interweaving trophic, environmental DNA and traditional survey‐based techniques, we show that the DNA‐assisted gut content analysis of a ubiquitous, easily accessible, generalist species may serve as a powerful, rapid and cost‐effective tool for large‐scale, routine estuarine biodiversity monitoring.     

Integrating 'top-down" and "bottom-up" mass spectrometric approaches for proteomic analysis of Shewanella oneidensis

Here we present a comprehensive method for proteome analysis that integrates both intact protein measurement ("top-down") and proteolytic fragment characterization ("bottom-up") mass spectrometric approaches, capitalizing on the unique capabilities of each method. This integrated approach was applied in a preliminary proteomic analysis of Shewanella oneidensis, a metal-reducing microbe of potential importance to the field of bioremediation. Cellular lysates were examined directly by the "bottom-up" approach as well as fractionated via anion-exchange liquid chromatography for integrated studies. A portion of each fraction was proteolytically digested, with the resulting peptides characterized by on-line liquid chromatography/tandem mass spectrometry. The remaining portion of each fraction containing the intact proteins was examined by high-resolution Fourier transform mass spectrometry. This "top-down" technique provided direct measurement of the molecular masses for the intact proteins and thereby enabled confirmation of post-translational modifications, signal peptides, and gene start sites of proteins detected in the "bottom-up" experiments. A total of 868 proteins from virtually every functional class, including hypotheticals, were identified from this organism.     

M-AMBI derived from taxonomic levels higher than species allows Ecological Status assessments of benthic habitats in new geographical areas

Under the Water Framework Directive (WFD) benthic Ecological Quality Ratios (EQRs) are important tools for assessing Ecological Status (ES) of coastal and transitional waters. Calculation of the Multivariate-AZTI Marine Biotic Index (M-AMBI) EQR is based on the proportions of sensitive and stress tolerant benthic invertebrate species, number of species and Shannon–Wiener diversity. The sensitivity of many tropical/sub-tropical taxa has not yet been determined, presenting a barrier to the direct transfer of WFD EQRs, and the ideas underpinning them, to the management of coastal waters beyond Europe. To overcome this we examine using higher taxonomic level data with M-AMBI.Before applying such approaches to assessing ES in new geographical regions it is essential to determine the effects of using higher taxonomic level data on M-AMBI in areas where the tool was developed. To this end, we use macrofaunal data from three well studied sites in north-western Europe to examine the effects of using taxonomic level data higher than species on M-AMBI. Using the European datasets M-AMBI ES classification was shown to be robust to changes in taxonomic level data. We test the suitability of family-level M-AMBI for assessing ES in subtropical Hong Kong waters. Family level M-AMBI was useful in detecting stress in Hong Kong, where it successfully detected temporal and spatial shifts in ES in response to seasonal hypoxia and salinity variability, and anthropogenic organic enrichment.     

Bottom-up and top-down drivers of herbivory on Arabica coffee along an environmental and management gradient

While sustainable agriculture relies on natural pest control, we lack insights into the relative importance of bottom-up and top-down factors on pest levels, especially along broad environmental and management gradients. To this aim, we focused on bottom-up and top-down control of herbivore damage in sixty sites in the centre of origin of Arabica coffee in southwestern Ethiopia, where coffee grows along a management gradient ranging from little or no management in the natural forest to commercial plantations. More specifically, we examined how canopy cover, percentage of surrounding forest and management intensity affected caffeine and chlorogenic acid concentration (bottom-up process) and attack of dummy caterpillars by ants and birds (top-down process), and how these in turn affected pest levels. Caffeine and chlorogenic acid concentrations were negatively related to canopy cover, while ant attack rate was positively related to canopy cover. Both ant and bird attack rate increased with the percentage of surrounding forest. Yet, secondary chemistry and caterpillar attack rates were unrelated to herbivory, and herbivory was only directly and positively affected by management intensity. Our study highlights that canopy cover can have contrasting effects on plant defence and predation, and that changes in bottom-up and top-down factors do – unlike often assumed – not necessarily translate into reduced pest levels. Instead, direct effects of management on pest levels may be more important than bottom-up or top-down mediated effects.