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Mathematical modelling is an essential tool in present-day ecological research. Yet for many ecologists it is still problematic to apply modelling in their research. In our experience, the major problem is at the conceptual level: proper understanding of what a model is, how ecological relations can be translated consistently into mathematical equations, how models are solved, steady states calculated and interpreted. Many textbooks jump over these conceptual hurdles to dive into detailed formulations or the mathematics of solution. This book attempts to fill that gap. It introduces essential concepts for mathematical modelling, explains the mathematics behind the methods, and helps readers to implement models and obtain hands-on experience. Throughout the book, emphasis is laid on how to translate ecological questions into interpretable models in a practical way.The book aims to be an introductory textbook at the undergraduate-graduate level, but will also be useful to seduce experienced ecologists into the world of modelling. The range of ecological models treated is wide, from Lotka-Volterra type of principle-seeking models to environmental or ecosystem models, and including matrix models, lattice models and sequential decision models. All chapters contain a concise introduction into the theory, worked-out examples and exercises. All examples are implemented in the open-source package R, thus taking away problems of software availability for use of the book. All code used in the book is available on a dedicated website.

Dissolved organic nitrogen (DON) acts as a large reservoir of fixed nitrogen. Whereas DON utilization is common in the microbial community, little is known about utilization by macrophytes. We investigated the ability of the coexisting temperate marine macrophytes Zostera noltii, Cymodocea nodosa, and Caulerpa prolifera to take up nitrogen and carbon from small organic substrates of different molecular complexities (urea, glycine, L-leucine, and L-phenylalanine) and from dissolved organic matter (DOM) derived from algal and bacterial cultures (substrates with a complex composition). In addition to inorganic nitrogen, nitrogen from small organic substrates could be taken up in significant amounts by all macrophytes. Substrate uptake by the aboveground tissue differed from that of the belowground tissue. No relationships between carbon and nitrogen uptake of small organics were found. The preference for individual organic substrates was related to their structural complexity and C:N ratio. Uptake of algae-derived organic nitrogen was of similar magnitude as inorganic nitrogen, and was preferred over bacteria-derived nitrogen. These results add to the growing evidence that direct or quick indirect DON utilization may be more widespread among aquatic macrophytes than traditionally thought. ; This research was supported by the regional government of Andalusia project FUNDIV (P07-RNM-2516), the Spanish Project CTM2008-00012/MAR, a European Reintegration Grant (MERG-CT-2007-205675), a travel grant from Schure-Beijerinck-Popping Fund (SBP/JK/2007-32) and the Netherlands Organization for Scientific Research. Thanks to Fidel Echevarrìa Navas (Director of CACYTMAR) for granting us access to facilities, and to Bas Koutstaal for helping with sample processing. We also thank the anonymous reviewers for their valuable comments which significantly improved this manuscript.

ABSTRACT Deep-sea sponges and their microbial symbionts transform various forms of carbon (C) and nitrogen (N) via several metabolic pathways, which, for a large part, are poorly quantified. Previous flux studies on the common deep-sea sponge Geodia barretti consistently revealed net consumption of dissolved organic carbon (DOC) and oxygen (O2) and net release of nitrate (NO−3). Here we present a biogeochemical metabolic network model that, for the first time, quantifies C and N fluxes within the sponge holobiont in a consistent manner, including many poorly constrained metabolic conversions. Using two datasets covering a range of individual G. barretti sizes (10–3,500 ml), we found that the variability in metabolic rates partially resulted from body size as O2 uptake allometrically scales with sponge volume. Our model analysis confirmed that dissolved organic matter (DOM), with an estimated C:N ratio of 7.7 ± 1.4, is the main energy source of G. barretti. DOM is primarily used for aerobic respiration, then for dissimilatory NO−3 reduction to ammonium (NH+4) (DNRA), and, lastly, for denitrification. Dissolved organic carbon (DOC) production efficiencies (production/assimilation) were estimated as 24 ± 8% (larger individuals) and 31 ± 9% (smaller individuals), so most DOC was respired to carbon dioxide (CO2), which was released in a net ratio of 0.77–0.81 to O2 consumption. Internally produced NH+4 from cellular excretion and DNRA fueled nitrification. Nitrification-associated chemoautotrophic production contributed 5.1–6.7 ± 3.0% to total sponge production. While overall metabolic patterns were rather independent of sponge size, (volume-)specific rates were lower in larger sponges compared to smaller individuals. Specific biomass production rates were 0.16% day–1 in smaller compared to 0.067% day–1 in larger G. barretti as expected for slow-growing deep-sea organisms. Collectively, our approach shows that metabolic modeling of hard-to-reach, deep-water sponges can be used to predict community-based ...

Local biodiversity trends over time are likely to be decoupled from global trends, as local processes may compensate or counteract global change. We analyze 161 long-term biological time series (15-91 years) collected across Europe, using a comprehensive dataset comprising similar to 6,200 marine, freshwater and terrestrial taxa. We test whether (i) local long-term biodiversity trends are consistent among biogeoregions, realms and taxonomic groups, and (ii) changes in biodiversity correlate with regional climate and local conditions. Our results reveal that local trends of abundance, richness and diversity differ among biogeoregions, realms and taxonomic groups, demonstrating that biodiversity changes at local scale are often complex and cannot be easily generalized. However, we find increases in richness and abundance with increasing temperature and naturalness as well as a clear spatial pattern in changes in community composition (i.e. temporal taxonomic turnover) in most biogeoregions of Northern and Eastern Europe. The global biodiversity decline might conceal complex local and group-specific trends. Here the authors report a quantitative synthesis of longterm biodiversity trends across Europe, showing how, despite overall increase in biodiversity metric and stability in abundance, trends differ between regions, ecosystem types, and taxa. ; Y We are grateful to the ILTER network and the eLTER PLUS project (Grand Agreement No. 871128) for financial support. We acknowledge the E-OBS dataset from the EUFP6 project ENSEMBLES (http://ensembles-eu.metoffice.com) and the data providers in the ECA&D project (http://www.ecad.eu).The evaluation of forest plant diversity was based on data collected by partners of the official UNECE ICP Forests Network (http://icp-forests.net/contributors); part of the data were co-financed by the European Commission, project LIFE 07 ENV/D/000218 "Further Development and Implementation of an EU-level Forest monitoring Systeme (FutMon)". Data on wintering water birds in Bulgaria were provided by the national Executive Environment Agency with the Ministry of Environment and Waters. Data from the Finnish moth monitoring scheme were supported by the Finnish Ministry of the Environment. Data from the Swedish ICP Integrated Monitoring sites were financed by the Swedish Environmental Protection Agency. Data collection at Esthwaite Water and a subset of UK ECN sites was supported by Natural Environment Research Council award number NE/R016429/1 as part of the UK-SCaPE programme delivering National Capability. Sponsorship of other UK ECN sites contributing data was provided by Agri-Food and Biosciences Institute, Biotechnology and Biological Sciences Research Council, Department of Environment Food and Rural Affairs, Natural Resources Wales, Defense Science Technology Laboratory, Environment Agency, Forestry Commission, Forest Research, the James Hutton Institute (The Rural & Environment Science & Analytical Services Division of the Scottish Government), Natural England, Rothamsted Research, Scottish Government, Scottish Natural Heritage and the Welsh Government. Data from the Mondego estuary (Portugal) were supported by the Centre for Functional Ecology Strategic Project (UID/BIA/04004/2019) within the PT2020 Partnership Agreement and COMPETE 2020, and by FEDER through the project ReNATURE (Centro 2020, Centro-01-765-0145-FEDER-000007). We would like to thank Limburgse Koepel voor Natuurstudie (LiKoNa) for the data related to the National Park Hoge Kempen (BE). We would like to acknowledge the support for the long-term monitoring program MONEOS in the Scheldt estuary (BE) by `De Vlaamse Waterweg' and `Maritieme Toegang' (Flemish government). We are grateful to the board of the National Park "De Hoge Veluwe" for the permission to conduct our research on their property. We thank Ian J. Winfield and Terje Bongard for contributing data for the sites: Bassenthwaite Lake, Derwent Water (UK) and Atna River (Norway, freshwater invertebrate time series). Open access funding provided by Umea University. ; Pilotto, F; Haase, P (corresponding author), Senckenberg Res Inst, Gelnhausen, Germany; Nat Hist Museum, Gelnhausen, Germany; Univ Duisburg Essen, Essen, Germany. francesca.pilotto@umu.se; francesca.pilotto@umu.se

Este artículo contiene 11 páginas, 2 tablas, 4 figuras. ; Local biodiversity trends over time are likely to be decoupled from global trends, as local processes may compensate or counteract global change. We analyze 161 long-term biological time series (15–91 years) collected across Europe, using a comprehensive dataset comprising ~6,200 marine, freshwater and terrestrial taxa. We test whether (i) local long-term biodiversity trends are consistent among biogeoregions, realms and taxonomic groups, and (ii) changes in biodiversity correlate with regional climate and local conditions. Our results reveal that local trends of abundance, richness and diversity differ among biogeoregions, realms and taxonomic groups, demonstrating that biodiversity changes at local scale are often complex and cannot be easily generalized. However, we find increases in richness and abundance with increasing temperature and naturalness as well as a clear spatial pattern in changes in community composition (i.e. temporal taxonomic turnover) in most biogeoregions of Northern and Eastern Europe. ; We are grateful to the ILTER network and the eLTER PLUS project (Grand Agreement No. 871128) for financial support. We acknowledge the E-OBS dataset from the EUFP6 project ENSEMBLES (http://ensembles-eu.metoffice.com) and the data providers in the ECA&D project (http://www.ecad.eu). The evaluation of forest plant diversity was based on data collected by partners of the official UNECE ICP Forests Network (http://icp-forests.net/contributors); part of the data were co-financed by the European Commission, project LIFE 07 ENV/D/000218 "Further Development and Implementation of an EU-level Forest monitoring Systeme (FutMon)". Data on wintering water birds in Bulgaria were provided by the national Executive Environment Agency with the Ministry of Environment and Waters. Data from the Finnish moth monitoring scheme were supported by the Finnish Ministry of the Environment. Data from the Swedish ICP Integrated Monitoring sites were financed by the Swedish Environmental Protection Agency. Data collection at Esthwaite Water and a subset of UK ECN sites was supported by Natural Environment Research Council award number NE/ R016429/1 as part of the UK-SCaPE programme delivering National Capability. Sponsorship of other UK ECN sites contributing data was provided by Agri-Food and Biosciences Institute, Biotechnology and Biological Sciences Research Council, Department of Environment Food and Rural Affairs, Natural Resources Wales, Defense Science Technology Laboratory, Environment Agency, Forestry Commission, Forest Research, the James Hutton Institute (The Rural & Environment Science & Analytical Services Division of the Scottish Government), Natural England, Rothamsted Research, Scottish Government, Scottish Natural Heritage and the Welsh Government. Data from the Mondego estuary (Portugal) were supported by the Centre for Functional Ecology Strategic Project (UID/BIA/04004/2019) within the PT2020 Partnership Agreement and COMPETE 2020, and by FEDER through the project ReNATURE (Centro 2020, Centro-01-765-0145-FEDER-000007). We would like to thank Limburgse Koepel voor Natuurstudie (LiKoNa) for the data related to the National Park Hoge Kempen (BE). We would like to acknowledge the support for the long-term monitoring program MONEOS in the Scheldt estuary (BE) by 'De Vlaamse Waterweg' and 'Maritieme Toegang' (Flemish government). We are grateful to the board of the National Park "De Hoge Veluwe" for the permission to conduct our research on their property. We thank Ian J. Winfield and Terje Bongard for contributing data for the sites: Bassenthwaite Lake, Derwent Water (UK) and Atna River (Norway, freshwater invertebrate time series). Open access funding provided by Umeå University. ; Peer reviewed