eDNA metabarcoding reveals the role of habitat specialization and spatial and environmental variability in shaping diversity patterns of fish metacommunities.

Information is scarce on how environmental and dispersal processes interact with biological features of the organisms, such as their habitat affinity, to influence patterns in biodiversity. We examined the role of habitat specialist vs. generalist species, and the spatial configuration, connectivity, and different environmental characteristics of river-floodplain habitats to get a more mechanistic understanding of alpha and beta diversity of fish metacommunities. We used environmental DNA metabarcoding to characterize species (taxa) richness and composition in two separate floodplains of the river Danube (Austria and Hungary) during two different hydrological conditions. Results showed that differences in the number of generalist and specialist species and their responses to connectivity and environmental gradients influenced patterns in alpha and beta diversity. Of the components of beta diversity, richness difference (nestedness) showed consistently higher values than replacement (turnover), mainly due to the decrease of specialist species along the connectivity gradient (i.e., from the mainstem to the most isolated oxbows). Variance in both alpha and beta diversity could be well predicted by a set of local and regional variables, despite high environmental variability, which characterizes river-floodplain ecosystems. Of these, the joint or shared variance fractions proved to be the most important, which indicates that the effects of local and regional processes cannot be unambiguously separated in these river-floodplain systems. Local scale environmental variables were more important determinants of both alpha and beta diversity in the low water period than in the high water period. These results indicate the differential role of local and regional processes in community organization during different hydrological conditions. Maintenance of both local and regional scale processes are thus important in the preservation of alpha and beta diversity of floodplain fish metacommunities, which should be considered by environmental management.

The effects of longitudinal fragmentation on riverine beta diversity are modulated by fragmentation intensity.

The loss of longitudinal connectivity affects river systems globally, being one of the leading causes of the freshwater biodiversity crisis. Barriers alter the dispersal of aquatic organisms and limit the exchange of species between local communities, disrupting metacommunity dynamics. However, the interplay between connectivity losses due to dams and other drivers of metacommunity structure, such as the configuration of the river network, needs to be explored. In this paper, we analyzed the response of fish communities to the network position and the fragmentation induced by dams while controlling for human pressures and environmental gradients. We studied three large European catchments covering a fragmentation gradient: Upper Danube (Austrian section), Ebro (Spain), and Odra/Oder (Poland). We quantified fragmentation through reach-scaled connectivity indices that account for the position of barriers along the dendritic network and the dispersal capacity of the organisms. We used generalized linear models to explain species richness and Local Contributions to Beta Diversity (LCBD) and multilinear regressions on the distance matrix to describe Beta Diversity and its Replacement and Richness Difference components. Results show that species richness was not affected by fragmentation. Network centrality metrics were relevant drivers of beta diversity for catchments with lower fragmentation (Ebro, Odra), and fragmentation indices were strong beta diversity predictors for the catchment with higher fragmentation (Danube). We conclude that in highly fragmented catchments, the effects of network centrality/isolation on biodiversity could be masked by the effects of dam fragmentation. In such catchments, metapopulation and metacommunity dynamics can be strongly altered by barriers, and the restoration of longitudinal connectivity (i.e. the natural centrality/isolation gradient) is urgent to prevent local extinctions.

Invasive forbs differ functionally from native graminoids, but are similar to native forbs.

• Exotic plant invasions can alter ecosystem processes, particularly if the invasive species are functionally different from native species. We investigated whether such alterations can be explained by differences in functional traits between native and invasive plants of the same functional group or by differences in functional group affiliation. • We compared six invasive forbs in Europe with six native forbs and six native graminoids in leaf and whole-plant traits, plasticity in response to nutrient supply and interspecific competition, litter decomposition rate, effects on soil nutrient availability, and allelopathy. All traits were measured in a series of pot experiments, and leaf traits additionally in the field. • Invasive forbs differed from native forbs for only a few traits; they had less leaf chlorophyll and lower phosphorus (P) uptake from soil, but they tended to have a stronger allelopathic effect. The invasive forbs differed in many traits from the native graminoids, their leaves had lower tissue densities and a shorter life span, their litter decomposed faster and they had a lower nitrogen-use efficiency. • Our results suggest that invasive forbs have the potential to alter ecosystem properties when invading graminoid-dominated and displacing native graminoids but not when displacing native forbs.

Two classes of functional connectivity in dynamical processes in networks.

The relationship between network structure and dynamics is one of the most extensively investigated problems in the theory of complex systems of recent years. Understanding this relationship is of relevance to a range of disciplines-from neuroscience to geomorphology. A major strategy of investigating this relationship is the quantitative comparison of a representation of network architecture (structural connectivity, SC) with a (network) representation of the dynamics (functional connectivity, FC). Here, we show that one can distinguish two classes of functional connectivity-one based on simultaneous activity (co-activity) of nodes, the other based on sequential activity of nodes. We delineate these two classes in different categories of dynamical processes-excitations, regular and chaotic oscillators-and provide examples for SC/FC correlations of both classes in each of these models. We expand the theoretical view of the SC/FC relationships, with conceptual instances of the SC and the two classes of FC for various application scenarios in geomorphology, ecology, systems biology, neuroscience and socio-ecological systems. Seeing the organisation of dynamical processes in a network either as governed by co-activity or by sequential activity allows us to bring some order in the myriad of observations relating structure and function of complex networks.

A multi-scale, integrative modeling framework for setting conservation priorities at the catchment scale for the Freshwater Pearl Mussel Margaritifera margaritifera.

The identification and prioritization of sites for conservation actions to protect biodiversity in lotic systems is crucial when economic resources or available areas are limited. Challenges include the incorporation of multi-scale interactions, and the application of species distribution models (SDMs) to rare organism with multiple life stages. To support the planning of conservation actions for the highly endangered Freshwater Pearl Mussel Margaritifera margaritifera (FPM), this paper aims at developing an ecohydrological modeling cascade including a hydrological model (SWAT) and a hydraulic model (HEC-RAS). Building on hydrology and hydraulics, Random Forest models for potential risk to juveniles due to sand accumulation, SDMs for adults habitat niche, and a landscape connectivity assessment of dispersal potential were developed. The feasibility of such models integration was tested in the Aist catchment (630 km2) in Austria. The potential FPM habitat and the sand accumulation risk for the whole catchment were predicted with good accuracy. Results show that while the potentially suitable habitats for adults FPM cover 34% of the river network, only few habitat patches can maximize the dispersal potential (4% of the river network) and even less are showing limited impact of accumulations (3.5% of river network). No habitat patch that meets all the three criteria is available, suggesting approaches that target the patch-specific critical life stage-factors are promising for conservation.

Identification of conservation and restoration priority areas in the Danube River based on the multi-functionality of river-floodplain systems.

Large river-floodplain systems are hotspots of biodiversity and ecosystem services but are also used for multiple human activities, making them one of the most threatened ecosystems worldwide. There is wide evidence that reconnecting river channels with their floodplains is an effective measure to increase their multi-functionality, i.e., ecological integrity, habitats for multiple species and the multiple functions and services of river-floodplain systems, although, the selection of promising sites for restoration projects can be a demanding task. In the case of the Danube River in Europe, planning and implementation of restoration projects is substantially hampered by the complexity and heterogeneity of the environmental problems, lack of data and strong differences in socio-economic conditions as well as inconsistencies in legislation related to river management. We take a quantitative approach based on best-available data to assess biodiversity using selected species and three ecosystem services (flood regulation, crop pollination, and recreation), focused on the navigable main stem of the Danube River and its floodplains. We spatially prioritize river-floodplain segments for conservation and restoration based on (1) multi-functionality related to biodiversity and ecosystem services, (2) availability of remaining semi-natural areas and (3) reversibility as it relates to multiple human activities (e.g. flood protection, hydropower and navigation). Our approach can thus serve as a strategic planning tool for the Danube and provide a method for similar analyses in other large river-floodplain systems.

Social equity shapes zone-selection: Balancing aquatic biodiversity conservation and ecosystem services delivery in the transboundary Danube River Basin.

Freshwater biodiversity is declining, despite national and international efforts to manage and protect freshwater ecosystems. Ecosystem-based management (EBM) has been proposed as an approach that could more efficiently and adaptively balance ecological and societal needs. However, this raises the question of how social and ecological objectives can be included in an integrated management plan. Here, we present a generic model-coupling framework tailored to address this question for freshwater ecosystems, using three components: biodiversity, ecosystem services (ESS), and a spatial prioritisation that aims to balance the spatial representation of biodiversity and ESS supply and demand. We illustrate this model-coupling approach within the Danube River Basin using the spatially explicit, potential distribution of (i) 85 fish species as a surrogate for biodiversity as modelled using hierarchical Bayesian models, and (ii) four estimated ESS layers produced by the Artificial Intelligence for Ecosystem Services (ARIES) platform (with ESS supply defined as carbon storage and flood regulation, and demand specified as recreation and water use). These are then used for (iii) a joint spatial prioritisation of biodiversity and ESS employing Marxan with Zones, laying out the spatial representation of multiple management zones. Given the transboundary setting of the Danube River Basin, we also run comparative analyses including the country-level purchasing power parity (PPP)-adjusted gross domestic product (GDP) and each country's percent cover of the total basin area as potential cost factors, illustrating a scheme for balancing the share of establishing specific zones among countries. We demonstrate how emphasizing various biodiversity or ESS targets in an EBM model-coupling framework can be used to cost-effectively test various spatially explicit management options across a multi-national case study. We further discuss possible limitations, future developments, and requirements for effectively managing a balance between biodiversity and ESS supply and demand in freshwater ecosystems.

Linking biodiversity to ecosystem services supply: Patterns across aquatic ecosystems.

Global initiatives have been increasingly focusing on mainstreaming the values of biodiversity and ecosystem services into decision-making at all levels. Due to the accelerated rate at which biodiversity is declining and its consequences for the functioning of ecosystems and subsequently, the services they provide, there is need to develop comprehensive assessments of the services and the benefits nature delivers to society. Based on expert evaluation, we identified relevant flow linkages in the supply-side of the socio-ecological system, i.e. from biodiversity to ecosystem services supply for eight case studies across European aquatic ecosystems covering freshwater, transitional, coastal and marine waters realms. Biological mediated services were considered, as well as those reliant on purely physical aspects of the ecosystem, i.e. abiotic outputs, since both have implications for spatial planning, management and decision-making. Due to the multidimensional nature of ecosystems and their biodiversity, our approach used ecosystem components such as habitats and biota as proxies for biodiversity and as the focal point for linkage identification. Statistical analysis revealed the importance of considering mobile biota in the spatial assessment of habitats. Contrary to literature evidences so far, our results showed significantly different and complementary ecosystem services supply patterns across the continuum of aquatic realms. The implemented score of ecosystem services supply has a high potential for integrated aquatic ecosystem service supply assessments in the context of ecosystem-based management.

Purification and characterization of the L-Ara4N transferase protein ArnT from Salmonella typhimurium.

The covalent addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) groups to lipid A, which resides in the outer membranes of bacteria such as Salmonella typhimurium and Escherichia coli, is the final step in the polymyxin-resistance pathway in these organisms. This modification is catalyzed by the inner membrane protein 4-amino-4-deoxy-L-arabinose transferase (ArnT). Little is known about the ArnT protein structure because it has not previously been purified. We report here the first expression and purification of 6 x His-tagged S. typhimurium ArnT in NovaBlue cells. The enzyme was purified using sequential Q-Sepharose anion exchange and HisLink nickel affinity column chromatography. The purified protein has an apparent molecular weight of 62 kDa on SDS-PAGE and the identity of the purified ArnT was confirmed by Western blot using a monoclonal antibody against the His-tag and by MALDI-TOF mass spectrometry. Purified ArnT protein was shown to be highly alpha-helical as determined by circular dichroism analysis. A chromosomal ArnT knockout strain of E. coli BL21(DE3) was developed to allow in vivo functional analysis of plasmid-encoded ArnT constructs, and a polymyxin assay was used to confirm that the cloned ArnT proteins retained full activity. These studies provide an essential foundation for further analysis of ArnT structure and function using mutagenesis and biophysical techniques.

Resting state conformation of the MsbA homodimer as studied by site-directed spin labeling.

MsbA is the ABC transporter for lipid A and is found in the inner membranes of Gram-negative bacteria such as Escherichia coli. Without MsbA present, bacterial cells accumulate a toxic amount of lipid A within their inner membranes. A crystal structure of MsbA was recently obtained that provides an excellent starting point for functional dynamics studies in membranes [Chang, and Roth (2001) Science 293, 1793-1800]. Although a structure of MsbA is now available, many questions remain concerning its mechanism of transport. Site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy is a powerful approach for characterizing local areas within a large protein structure in addition to detecting and following changes in local structure due to dynamic interactions within a protein. The quaternary structure of the resting state of the MsbA homodimer reconstituted into lipid membranes has been evaluated by SDSL EPR spectroscopy and chemical cross-linking techniques. SDSL and cross-linking results are consistent with the controversial resting state conformation of the MsbA homodimer found in the crystal structure, with the tips of the transmembrane helices forming a dimer interface. The position of MsbA in the membrane bilayer along with the relative orientation of the transmembrane helical bundles with respect to one another has been determined. Characterization of the resting state of the MsbA homodimer is essential for future studies on the functional dynamics of this membrane transporter.