Highlights from the perspectives in melanoma XII conference

The following meeting highlights are from the Perspectives in Melanoma XII conference, held in Scheveningen/The Hague, the Netherlands, on October 2–4, 2008. Selected reviews are included but further discussions of these and other presentations are posted at http://www.MelanomaCare.org .     

Beyond the single index: Investigating ecological mechanisms underpinning ecosystem multifunctionality with network analysis

Ecosystems simultaneously deliver multiple functions that relate to both the activities of resident species and environmental conditions. One of the biggest challenges in multifunctionality assessment is balancing analytical simplicity with ecosystem complexity. As an alternative to index‐based approaches, we introduce a multivariate network analysis that uses network theory to assess multifunctionality in terms of the relationships between species'' functional traits, environmental characteristics, and functions. We tested our approach in a complex and heterogeneous ecosystem, marine intertidal sandflats. We considered eight ecosystem function, five macrofaunal functional trait groups derived from 36 species, and four environmental characteristics. The indicators of ecosystem functions included the standing stock of primary producers, oxygen production, benthic oxygen consumption, DIN (ammonium and NOx efflux) and phosphate release from the sediments, denitrification, and organic matter degradation at the sediment surface. Trait clusters included functional groups of species that shared combinations of biological traits that affect ecosystem function: small mobile top 2 cm dwellers, suspension feeders, deep‐dwelling worms, hard‐bodied surface dwellers, and tube‐forming worms. Environmental characteristics included sediment organic matter, %mud, %shell hash, and %sediment water content. Our results visualize and quantify how multiple ecosystem elements are connected and contribute to the provision of functions. Small mobile top 2 cm dwellers (among trait clusters) and %mud (among environmental characteristics) were the best predictor for multiple functions. Detailed knowledge of multifunctionality relationships can significantly increase our understanding of the real‐world complexity of natural ecosystems. Multivariate network analysis, as a standalone method or applied alongside already existing single index multifunctionality methods, provides means to advance our understanding of how environmental change and biodiversity loss can influence ecosystem performance across multiple dimensions of functionality. Embedding such a detailed yet holistic multifunctionality assessment in environmental decision‐making will support the assessment of multiple ecosystem services and social‐ecological values.     

International conference on “Photosynthesis research for sustainability-2013: in honor of Jalal A. Aliyev”, held during June 5–9, 2013, Baku, Azerbaijan

In this brief report, we provide a pictorial essay on an international conference “Photosynthesis Research for Sustainability-2013 in honor of Jalal A. Aliyev” that was held in Baku, Azerbaijan, during June 5–9, 2013 (http://photosynthesis2013.cellreg.org/). We begin this report with a brief note on Jalal Aliyev, the honored scientist, and on John Walker (1997 Nobel laureate in Chemistry) who was a distinguished guest and lecturer at the Conference. We briefly describe the Conference, and the program. In addition to the excellent scientific program, a special feature of the Conference was the presentation of awards to nine outstanding young investigators; they are recognized in this report. We have also included several photographs to show the pleasant ambience at this conference. (See http://photosynthesis2013.cellreg.org/Photo-Gallery.php; https://www.dropbox.com/sh/qcr124dajwffwh6/TlcHBvFu4H?m; and https://www.copy.com/s/UDlxb9fgFXG9/Baku for more photographs taken by the authors as well as by others.) We invite the readers to the next conferences on “Photosynthesis Research for Sustainability—2014: in honor of Vladimir A. Shuvalov” to be held during June 2–7, 2014, in Pushchino, Russia. Detailed information for this will be posted at the Website: http://photosynthesis2014.cellreg.org/, and for the subsequent conference on “Photosynthesis Research for Sustainability—2015” to be held in May or June 2015, in Baku, Azerbaijan, at http://photosynthesis2015.cellreg.org/.     

Carbon cycling and budget in a forested basin of southwestern Hokkaido,northern Japan

Quantification of annual carbon sequestration is very important in order to assess the function of forest ecosystems in combatting global climate change and the ecosystem responses to those changes. Annual cycling and budget of carbon in a forested basin was investigated to quantify the carbon sequestration of a cool-temperate deciduous forest ecosystem in the Horonai stream basin, Tomakomai Experimental Forest, northern Japan. Net ecosystem exchange, soil respiration, biomass increment, litterfall, soil-solution chemistry, and stream export were observed in the basin from 1999–2001 as a part of IGBP-TEMA project. We found that 258 g C m^–2 year^–1 was sequestered annually as net ecosystem exchange (NEE) in the forested basin. Discharge of carbon to the stream was 4 g C m^–2 year^–1 (about 2% of NEE) and consisted mainly of dissolved inorganic carbon (DIC). About 43% of net ecosystem productivity (NEP) was retained in the vegetation, while about 57% of NEP was sequestered in soil, suggesting that the movement of sequestered carbon from aboveground to belowground vegetation was an important process for net carbon accumulation in soil. The derived organic carbon from aboveground vegetation that moved to the soil mainly accumulated in the solid phase of the soil, with the result that the export of dissolved organic carbon to the stream was smaller than that of dissolved inorganic carbon. Our results indicated that the aboveground and belowground interaction of carbon fluxes was an important process for determining the rate and retention time of the carbon sequestration in a cool-temperate deciduous forest ecosystem in the southwestern part of Hokkaido, northern Japan.     

‘Life after last orders’: microbiology as a career

The 2003 conference of the International Biodegradation and Biodeterioration Society (www.biodeterioration. org) and the International Biodegradation Research Group (www.ibrg.org), was held last September at the Manchester Metropolitan University. The conference, ‘Management and Control of Undesirable Microorganisms’, followed the usual format of lectures, questions, posters and social events, but an additional event was staged for younger society members. Funding from FEMS, the Federation of European Microbiology Societies, in the form of a Young Scientists Grant, enabled the attendance of delegates from across Europe including the Czech Republic, Latvia, Germany, Russia, Uzbekistan and the UK. These delegates, and the rest of the conference, were invited to a workshop entitled ‘Life after Last Orders’, where some of the slightly older members of the Society described their career paths. Informal 5–10 minute presentations were followed by question/answer sessions, which also included some interesting contributions from the floor. The session was chaired by the two youngest members of IBBS Council, Kathryn Whitehead, a PhD student at MMU, and Chris van der Gast, from the University of Oxford Centre for Environmental Biotechnology. The following narratives describe the career paths of two ‘experienced’ microbiologists! It was fascinating to hear how the careers of one's peers had developed.     

Structural and functional development of twelve newly established floodplain pond mesocosms

Ecosystems are complex structures with interacting abiotic and biotic processes evolving with ongoing succession. However, limited knowledge exists on the very initial phase of ecosystem development and colonization. Here, we report results of a comprehensive ecosystem development monitoring for twelve floodplain pond mesocosms (FPM; 23.5 m × 7.5 m × 1.5 m each) located in south‐western Germany. In total, 20 abiotic and biotic parameters, including structural and functional variables, were monitored for 21 months after establishment of the FPMs. The results showed evolving ecosystem development and primary succession in all FPMs, with fluctuating abiotic conditions over time. Principal component analyses and redundancy analyses revealed season and succession time (i.e., time since ecosystem establishment) to be significant drivers of changes in environmental conditions. Initial colonization of both aquatic (i.e., water bodies) and terrestrial (i.e., riparian land areas) parts of the pond ecosystems occurred within the first month, with subsequent season‐specific increases in richness and abundance for aquatic and terrestrial taxa over the entire study period. Abiotic environmental conditions and aquatic and terrestrial communities showed increasing interpond variations over time, that is, increasing heterogeneity among the FPMs due to natural environmental divergence. However, both functional variables assessed (i.e., aquatic and terrestrial litter decomposition) showed opposite patterns as litter decomposition rates slightly decreased over time and interpond differences converged with successional ecosystem developments. Overall, our results provide rare insights into the abiotic and biotic conditions and processes during the initial stages of freshwater ecosystem formation, as well as into structural and functional developments of the aquatic and terrestrial environment of newly established pond ecosystems.     

A method for lake ecosystem health assessment: an Ecological Modeling Method (EMM) and its application

Ecosystem health is a newly proposed concept that sets new goals for environmental management. Its definition, indexing and assessment methods are still being perfected. An Ecological Modeling Method (EMM) for lake ecosystem health assessment is proposed in this paper. The EMM's procedures are: (1) to analyze the ecosystem structure of a lake in order to determine the structure and complexity of the lake's ecological model; (2) to develop a model having ecological health indicators, by designing a conceptual diagram, establishing model equations, estimating model parameters and being integrated with ecological indicators; (3) to compare the simulated and observed values of important state variables and process rates (i.e. model calibration) in order to evaluate the applicability of the model to lake ecosystem health assessment; (4) to calculate ecosystem health indicators based on the developed model; and (5) to assess lake ecosystem health according to the values of the ecosystem health indicators. The EMM was applied, as a case study, to the ecosystem health assessment of a eutrophic Chinese lake (Lake Chao) between April 1987 and March 1988. A relative order of health states from poor to good was determined as follows: August–October 1987 > April–May 1987 > June–July 1987 > November–December 1987 > January–March 1988. These results compared quite favourably with the actual current conditions at Lake Chao. The EMM method, therefore, was suitable in assessing lake ecosystem health at Lake Chao.     

Beetles (Insecta: Coleoptera) as bioindicators of the assessment of environmental pollution

Bioindicators have been generating great interest in environmental pollution research. Insects and especially arthropod are useful to assess the effects of anthropogenic activities on the terrestrial ecosystem, because they are inclose contact with toxic elements present in soil and in leaf litter. Beetles are extremely sensitive to several ecological parameters, react quickly to environmental modifications and can be easily and cost-effectively sampled by various methods. These criteria make beetles excellent indicators of terrestrial ecosystem. In order to evaluate the environmental impact of human activities on different ecosystems, the use of Coleoptera in ecological studies has been largely increased in recent years.

This review presents the results obtained by researchers when using beetles as bioindicators of metallic pollution and forest disturbance.     

Integrated Assessment of Large-Scale Biofuel Production

This paper proposes a different framework for discussing the possibility of replacing a significant fraction of fossil energy consumption of modern economies with biofuels. The proposed analysis is not based on the two classic feasibility checks—land availability and output/input energy ratio—debated in the majority of the literature in this field. Rather, the focus is on the desirability of an energy sector powered by biomass energy. Discussing of desirability requires introducing a multicriteria approach, that in turn requires a definition of a set of criteria of performance for such an energy sector. The concepts of societal metabolism and ecosystem metabolism are introduced to define five criteria of performance for an energy sector powered by alternative sources.

This paper does not tell the society whether or not biofuels should be used to replace fossil energy. Rather, it proposes a method of characterization of pros and cons for the option biofuel which can be used to make more informed choices. An analysis of three systems of production—corn-ethanol, sunflower-biodiesel, and SRWC-methanol—is provided to indicate the existence of systemic characteristics associated with an energy sector powered by biofuels. These characteristics are likely to persist even when different technical coefficients will be achieved. The conclusion is that, at the moment, it is not possible to replace the actual performance of an energy sector based on fossil energy with an energy sector running on biofuel. Biomass energy can and will have to play an important role in the sustainability of humankind, but this will require a better understanding of (i) the role that an energy sector plays within a given structure of societal metabolism; and (ii) the impact generated on ecosystem metabolism by societal metabolism, plus a lot of wisdom.     

A model of a digital biological ecosystem

In this paper, we propose a model of a digital biological ecosystem of fish. Collections of fish data by scientists in Malaysia have been converted and developed into a digital biological ecosystem using computational technology and methods. We used a combination of Geographical Information System, databases and ontologies for storing, retrieving and visualizing fish species distribution and their abundance as well as their relationship with the environment. We used ArcGIS to build the fish and environmental geodatabase, which is linked to Google Earth for real-time visualization, and Surfer 8 to create contour maps which are superimposed as layers on the ArcGIS interface. Individual fish species on the map are hyperlinked to the FishBase Portal (http://www.fishbase.org/) while the published map is displayed using ArcReader. The three databases that we created contain information about fish species, environment and contours. These are also integrated using a fish ontology which will link all the available information for various fish species. The proposed system can be adopted by marine scientists to better convince economists, fishery managers, coastal developers and government bodies who make important decisions on conservation policies and laws.     

Metaproteomic data analysis at a glance: advances in computational microbial community proteomics

Introduction: Within the last decade, the study of microbial communities has gained increasing research interest also driven by the recognition of the important role of these consortia in human health and disease. Metaproteomics, the analysis of the entire set of proteins from all microorganisms present in one ecosystem, has become a prominent technique for studying the relation between taxonomic diversity and functional profile of microbial communities.

Areas covered: The aim of this review is to address opportunities and challenges of metaproteomics from a computational perspective. Appealing to an audience of microbial ecologists and proteomic researchers alike, we provide an overview on state-of-the-art software and databases by which metaproteome data can be readily analyzed.

Expert commentary: While tailored protein databases, combined search algorithms and iterative workflows are means to improve the identification yield, software tools for taxonomic and functional analysis are challenged by the vast amount of unannotated sequences in metaproteomics.     

Predictive markers of safety and immunogenicity of adjuvanted vaccines

Vaccination represents one of the greatest public health triumphs; in part due to the effect of adjuvants that have been included in vaccine preparations to boost the immune responses through different mechanisms. Although a variety of novel adjuvants have been under development, only a limited number have been approved by regulatory authorities for human vaccines. This report reflects the conclusions of a group of scientists from academia, regulatory agencies and industry who attended a conference on the current state of the art in the adjuvant field. Held at the U.S. Pharmacopeial Convention (USP) in Rockville, Maryland, USA, from 18 to 19 April 2013 and organized by the International Association for Biologicals (IABS), the conference focused particularly on the future development of effective adjuvants and adjuvanted vaccines and on overcoming major hurdles, such as safety and immunogenicity assessment, as well as regulatory scrutiny. More information on the conference output can be found on the IABS website, http://www.iabs.org/.     

The quest for a mechanistic understanding of biodiversity–ecosystem services relationships

Ecosystem services (ES) approaches to biodiversity conservation are currently high on the ecological research and policy agendas. However, despite a wealth of studies into biodiversity''s role in maintaining ES (B–ES relationships) across landscapes, we still lack generalities in the nature and strengths of these linkages. Reasons for this are manifold, but can largely be attributed to (i) a lack of adherence to definitions and thus a confusion between final ES and the ecosystem functions (EFs) underpinning them, (ii) a focus on uninformative biodiversity indices and singular hypotheses and (iii) top-down analyses across large spatial scales and overlooking of context-dependency. The biodiversity–ecosystem functioning (B–EF) field provides an alternate context for examining biodiversity''s mechanistic role in shaping ES, focusing on species'' characteristics that may drive EFs via multiple mechanisms across contexts. Despite acknowledgements of a need for B–ES research to look towards underlying B–EF linkages, the connections between these areas of research remains weak. With this review, we pull together recent B–EF findings to identify key areas for future developments in B–ES research. We highlight a means by which B–ES research may begin to identify how and when multiple underlying B–EF relationships may scale to final ES delivery and trade-offs.     

A practical guide to the application of the IUCN Red List of Ecosystems criteria

The newly developed IUCN Red List of Ecosystems is part of a growing toolbox for assessing risks to biodiversity, which addresses ecosystems and their functioning. The Red List of Ecosystems standard allows systematic assessment of all freshwater, marine, terrestrial and subterranean ecosystem types in terms of their global risk of collapse. In addition, the Red List of Ecosystems categories and criteria provide a technical base for assessments of ecosystem status at the regional, national, or subnational level. While the Red List of Ecosystems criteria were designed to be widely applicable by scientists and practitioners, guidelines are needed to ensure they are implemented in a standardized manner to reduce epistemic uncertainties and allow robust comparisons among ecosystems and over time. We review the intended application of the Red List of Ecosystems assessment process, summarize ‘best-practice’ methods for ecosystem assessments and outline approaches to ensure operational rigour of assessments. The Red List of Ecosystems will inform priority setting for ecosystem types worldwide, and strengthen capacity to report on progress towards the Aichi Targets of the Convention on Biological Diversity. When integrated with other IUCN knowledge products, such as the World Database of Protected Areas/Protected Planet, Key Biodiversity Areas and the IUCN Red List of Threatened Species, the Red List of Ecosystems will contribute to providing the most complete global measure of the status of biodiversity yet achieved.     

Meta-ecosystem dynamics and functioning on finite spatial networks

The addition of spatial structure to ecological concepts and theories has spurred integration between sub-disciplines within ecology, including community and ecosystem ecology. However, the complexity of spatial models limits their implementation to idealized, regular landscapes. We present a model meta-ecosystem with finite and irregular spatial structure consisting of local nutrient–autotrophs–herbivores ecosystems connected through spatial flows of materials and organisms. We study the effect of spatial flows on stability and ecosystem functions, and provide simple metrics of connectivity that can predict these effects. Our results show that high rates of nutrient and herbivore movement can destabilize local ecosystem dynamics, leading to spatially heterogeneous equilibria or oscillations across the meta-ecosystem, with generally increased meta-ecosystem primary and secondary production. However, the onset and the spatial scale of these emergent dynamics depend heavily on the spatial structure of the meta-ecosystem and on the relative movement rate of the autotrophs. We show how this strong dependence on finite spatial structure eludes commonly used metrics of connectivity, but can be predicted by the eigenvalues and eigenvectors of the connectivity matrix that describe the spatial structure and scale. Our study indicates the need to consider finite-size ecosystems in meta-ecosystem theory.     

Ecosystem service benefits of contrasting conservation strategies in a human-dominated region

The hope among policy-makers and scientists alike is that conservation strategies designed to protect biodiversity also provide direct benefits to people by protecting other vital ecosystem services. The few studies that have examined the delivery of ecosystem services by existing conservation efforts have concentrated on large, ‘wilderness’-style biodiversity reserves. However, such reserves are not realistic options for densely populated regions. Here, we provide the first analyses that compare representation of biodiversity and three other ecosystem services across several contrasting conservation strategies in a human-dominated landscape (England). We show that small protected areas and protected landscapes (restrictive zoning) deliver high carbon storage and biodiversity, while existing incentive payment (agri-environment) schemes target areas that offer little advantage over other parts of England in terms of biodiversity, carbon storage and agricultural production. A fourth ecosystem service—recreation—is under-represented by all three strategies. Our findings are encouraging as they illustrate that restrictive zoning can play a major role in protecting natural capital assets in densely populated regions. However, trade-offs exist even among the four ecosystem services we considered, suggesting that a portfolio of conservation and sustainability investments will be needed to deliver both biodiversity and the other ecosystem services demanded by society.     

The development of ecosystem objectives for the Laurentian Great Lakes

Historically management of human use of ecosystems has been based around engineering and chemical approaches and through the construction of treatment facilities, effluent controls and setting chemical concentrations, both at end of pipe and in the aquatic environment. However, the general continued degradation of many ecosystems shows these approaches alone are insufficient. In the Laurentian Great Lakes the Great Lakes Water Quality Agreement was first signed in 1972 and ratified in 1978 and in 1987 tacitly acknowledged the problems with a chemical only approach by requiring the development of ecosystem objectives in the 1978 agreement. Furthermore, the agreement specifically identified numerical ecosystem objectives in the 1987 agreement. The evolution of ecosystem objectives in the Great Lakes has expanded from the strictly numerical objectives such as production of lake trout and abundance of the amphipod Pontoporeia hoyi. More recent developments in ecosystem objectives have been the inclusion of indicators for wildlife, habitat, human health and stewardship.Prepared as a discussion paper presented to the United Nations Economic Commission for Europe's seminar on an Ecosystems Approach to Water Management (May 27–31, 1991).     

生态恢复中生态系统服务的演变:趋势、过程与评估

经过10余年的发展,生态系统服务已经成为生态恢复研究关注的前沿和热点。生态恢复改变了生态系统格局与过程,对生态系统服务的产生和提供具有重要影响。但是目前对于生态系统服务在生态恢复过程中的演化仍缺少系统性研究。对国内外相关研究的最新成果进行综述,总结了生态系统服务评估中框架的构建和方法的选择(参数转移法、系统模型法和定量指标法),介绍了生态恢复对生态系统服务的促进作用、生态系统服务的演变过程以及不同生态系统服务间的协同与权衡关系,分析了社会经济因素对生态恢复和生态系统服务维持的影响。最后结合我国生态恢复实践,提出未来生态恢复和生态系统服务研究可以从深化作用机制研究、推动服务评估创新、增强研究成果应用3方面深化和拓展。     

Submarine groundwater discharge alters coral reef ecosystem metabolism

Submarine groundwater discharge (SGD) influences near-shore coral reef ecosystems worldwide. SGD biogeochemistry is distinct, typically with higher nutrients, lower pH, cooler temperature and lower salinity than receiving waters. SGD can also be a conduit for anthropogenic nutrients and other pollutants. Using Bayesian structural equation modelling, we investigate pathways and feedbacks by which SGD influences coral reef ecosystem metabolism at two Hawai''i sites with distinct aquifer chemistry. The thermal and biogeochemical environment created by SGD changed net ecosystem production (NEP) and net ecosystem calcification (NEC). NEP showed a nonlinear relationship with SGD-enhanced nutrients: high fluxes of moderately enriched SGD (Wailupe low tide) and low fluxes of highly enriched SGD (Kūpikipiki''ō high tide) increased NEP, but high fluxes of highly enriched SGD (Kūpikipiki''ō low tide) decreased NEP, indicating a shift toward microbial respiration. pH fluctuated with NEP, driving changes in the net growth of calcifiers (NEC). SGD enhances biological feedbacks: changes in SGD from land use and climate change will have consequences for calcification of coral reef communities, and thereby shoreline protection.     

Dissolved organic carbon and its utilization in a riverine wetland ecosystem

Variations in dissolved organic carbon (DOC) concentrations of surface waters and subsurface interstitial groundwater of riparian and wetland soils to 1.2 m depth were evaluated in a riverine wetland ecosystem over one year. DOC was monitored at seven sites within the wetland pond, two sites on the inflow stream, and one site on the outflow stream. Surface concentrations in the inflow stream ranged from 0.74 to 11.6 mg C L^–1 and those of the outflow from 2.1 to 8.0 mg C L^–1 Average DOC from stream floodplain hydrosoils (3.1 to 32.1 mg C L^–1 was greater than DOC from the sediments below the stream channel (1.6 to 6.8 mg C L^–1 Surface DOC within the wetland varied seasonally, with greatest fluctuations in concentrations through the summer and autumn (range 4.8 to 32.6 mg C L^–1 ) during intensive macrophyte growth and bacterial production. DOC was less variable during the winter months (1.7 to 3.3 mg C L^–1 Within the wetland pond, average DOC concentrations (7.1 to 48.2 mg C L^–1) in the subsurface waters were significantly greater (p < 0.05) than average surface concentrations. The microbial availability of surface and subsurface DOC to bacteria was evaluated from losses of DOC by wetland bacteria grown on the DOC. Bacterial growth efficiencies ranged from 5 to 20% and were negatively correlated to the percentage of DOC removed by bacteria (r²=0.93). Throughout the ecosystem, DOC concentrations were greatest in the subsurface waters, but at most depths this DOC was a less suitable substrate than surface DOC for utilization by bacteria.