Contrasting effects of low‐level phosphorus and nitrogen enrichment on growth of the mat‐forming alga Didymosphenia geminata in an oligotrophic river

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Spider web guilds in cacao agroforestry – comparing tree,plot and landscape‐scale management

Aim Owing to their role as insect predators, web‐building spiders can be important biological control agents within agricultural systems. In complex tropical agroecosystems such as agroforests, management determines plant architecture, vegetation composition and associated ant density, but little is known on how these attributes, together with landscape context, determine spider web density. We hypothesized that all three spatial scales and the presence of Philidris ants significantly contribute to the explanation of spider web density with web types being differently affected. Location In 42 differently managed cacao agroforestry systems in Sulawesi, Indonesia. Methods We surveyed the distribution of five spider‐web types on 420 cacao trees to determine how these relate to habitat variables and a numerically dominant ant species at three different spatial scales, comparing tree, plot and landscape features. We fitted linear mixed‐effects model, selected the best model subset using information‐theoretic criteria and calculated the model‐averaged estimates. We used non‐metric multidimensional scaling (NMDS) to determine and visualize guild level responses to the effects of the tree, plot and landscape‐scale variables. Results The five spider guilds preferred different features of cacao tree architecture. Most frequently recorded webs belonged to the line‐ and orb‐web type. At the tree scale, overall web density was positively related to canopy openness. At the plot scale, a higher number of shade trees was related to a higher web density. At the landscape scale, the altitude determined the distribution patterns of web‐building spiders. Presence of Philidris ants was positively associated with density of orb webs, while no pattern was found for other web types. Main conclusions Results suggest spider web density could be increased by pruning of cacao trees while keeping shade trees at high density in cacao plots. The results emphasize the need to consider scale dependency of crop management and web‐guild‐specific responses that may be related to different functional roles of spiders as a high‐density predator group in agroforestry.     

Identifying the interacting roles of stressors in driving the global loss of canopy‐forming to mat‐forming algae in marine ecosystems

Identifying the type and strength of interactions between local anthropogenic and other stressors can help to set achievable management targets for degraded marine ecosystems and support their resilience by identifying local actions. We undertook a meta‐analysis, using data from 118 studies to test the hypothesis that ongoing global declines in the dominant habitat along temperate rocky coastlines, forests of canopy‐forming algae and/or their replacement by mat‐forming algae are driven by the nonadditive interactions between local anthropogenic stressors that can be addressed through management actions (fishing, heavy metal pollution, nutrient enrichment and high sediment loads) and other stressors (presence of competitors or grazers, removal of canopy algae, limiting or excessive light, low or high salinity, increasing temperature, high wave exposure and high UV or CO₂), not as easily amenable to management actions. In general, the cumulative effects of local anthropogenic and other stressors had negative effects on the growth and survival of canopy‐forming algae. Conversely, the growth or survival of mat‐forming algae was either unaffected or significantly enhanced by the same pairs of stressors. Contrary to our predictions, the majority of interactions between stressors were additive. There were however synergistic interactions between nutrient enrichment and heavy metals, the presence of competitors, low light and increasing temperature, leading to amplified negative effects on canopy‐forming algae. There were also synergistic interactions between nutrient enrichment and increasing CO₂ and temperature leading to amplified positive effects on mat‐forming algae. Our review of the current literature shows that management of nutrient levels, rather than fishing, heavy metal pollution or high sediment loads, would provide the greatest opportunity for preventing the shift from canopy to mat‐forming algae, particularly in enclosed bays or estuaries because of the higher prevalence of synergistic interactions between nutrient enrichment with other local and global stressors, and as such it should be prioritized.     

Colonization–extinction dynamics of epixylic lichens along a decay gradient in a dynamic landscape

Metapopulation models are often used for understanding and predicting species dynamics in fragmented landscapes. Several models have been proposed depending on e.g. the relative importance of patch dynamics on the metapopulation dynamics. Dead wood is a dynamic substrate patch, and species that are confined to such patches have experienced a high degree of habitat loss in managed forests. Little is, however, known about how the population dynamics of epixylic species are affected by the fast dynamics of their substrate patches. We quantified the effect of local patch conditions and metapopulation processes on colonizations and extinctions of epixylic lichen species in a managed boreal forest landscape. This was done by twice surveying seven lichen metapopulations on 293 stumps in 30 stands of ages covering the duration of the dynamic patches (stumps). We also investigated the relative importance of local stochastic extinctions from stumps that remained available, and deterministic extinctions due to stump surface disappearance. We found importance of a decay gradient, surrounding metapopulation size, and local population sizes, in driving the colonization–extinction dynamics of epixylic lichens. The species were sorted along the stump decay gradient. Increasing surrounding metapopulation size was associated with increased colonization rates, and increasing local population size decreased lichen extinction rates. Finally, both local stochastic extinctions and deterministic extinctions due to patch disappearance occur, confirming that the long‐term persistence of epixylic lichens depends on colonization rates that compensate for stochastic population extinctions as well as deterministic extinctions.     

Predicting food‐web structure with metacommunity models

Synthesis Metacommunity theory aims to elucidate the relative influence of local and regional‐scale processes in generating diversity patterns across the landscape. Metacommunity research has focused largely on assemblages of competing organisms within a single trophic level. Here, we test the ability of metacommunity models to predict the network structure of the aquatic food web found in the leaves of the northern pitcher plant Sarracenia purpurea. The species‐sorting and patch‐dynamics models most accurately reproduced nine food web properties, suggesting that local‐scale interactions play an important role in structuring Sarracenia food webs. Our approach can be applied to any well‐resolved food web for which data are available from multiple locations. The metacommunity framework explores the relative influence of local and regional‐scale processes in generating diversity patterns across the landscape. Metacommunity models and empirical studies have focused mostly on assemblages of competing organisms within a single trophic level. Studies of multi‐trophic metacommunities are predominantly restricted to simplified trophic motifs and rarely consider entire food webs. We tested the ability of the patch‐dynamics, species‐sorting, mass‐effects, and neutral metacommunity models, as well as three hybrid models, to reproduce empirical patterns of food web structure and composition in the complex aquatic food web found in the northern pitcher plant Sarracenia purpurea. We used empirical data to determine regional species pools and estimate dispersal probabilities, simulated local food‐web dynamics, dispersed species from regional pools into local food webs at rates based on the assumptions of each metacommunity model, and tested their relative fits to empirical data on food‐web structure. The species‐sorting and patch‐dynamics models most accurately reproduced nine food web properties, suggesting that local‐scale interactions were important in structuring Sarracenia food webs. However, differences in dispersal abilities were also important in models that accurately reproduced empirical food web properties. Although the models were tested using pitcher‐plant food webs, the approach we have developed can be applied to any well‐resolved food web for which data are available from multiple locations.     

One short cysteine‐rich sequence pattern – two different disulfide‐bonded structures – a molecular dynamics simulation study

The nematocyst walls of Hydra are formed by proteins containing small cysteine‐rich domains (CRDs) of ~25 amino acids. The first CRD of nematocyst outer all antigen (NW1) and the C‐terminal CRD of minicollagen‐1 (Mcol1C) contain six cysteines at identical sequence positions, however adopt different disulfide bonded structures. NW1 shows the disulfide connectivities C2‐C14/C6‐C19/C10‐C18 and Mcol1C C2‐C18/C6‐C14/C10‐C19. To analyze if both show structural preferences in the open, non‐disulfide bonded form, which explain the formation of either disulfide connectivity pattern, molecular dynamics (MD) simulations at different temperatures were performed. NW1 maintained in the 100‐ns MD simulations at 283 K a rather compact fold that is stabilized by specific hydrogen bonds. The Mcol1C structure fluctuated overall more, however stayed most of the time also rather compact. The analysis of the backbone Φ/ψ angles indicated different turn propensities for NW1 and Mcol1C, which mostly can be explained based on published data about the influence of different amino acid side chains on the local backbone conformation. Whereas a folded precursor mechanism may be considered for NW1, Mcol1C may fold according to the quasi‐stochastic folding model involving disulfide bond reshuffling and conformational changes, locking the native disulfide conformations. The study further demonstrates the power of MD simulations to detect local structural preferences in rather dynamic systems such as the open, non‐disulfide bonded forms of NW1 and Mcol1C, which complement published information from NMR backbone residual dipolar couplings. Because the backbone structural preferences encoded by the amino acid sequence embedding the cysteines influence which disulfide connectivities are formed, the data are generally interesting for a better understanding of oxidative folding and the design of disulfide stabilized therapeutics. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.     

Long‐term colonization ecology of forest‐dwelling species in a fragmented rural landscape – dispersal versus establishment

Species colonization in a new habitat patch is an efficiency indicator of biodiversity conservation. Colonization is a two‐step process of dispersal and establishment, characterized by the compatibility of plant traits with landscape structure and habitat conditions. Therefore, ecological trait profiling of specialist species is initially required to estimate the relative importance of colonization filters. Old planted parks best satisfy the criteria of a newly created and structurally matured habitat for forest‐dwelling plant species. We sampled species in 230 ancient deciduous forests (source habitat), 74 closed‐canopy manor parks (target habitats), 151 linear wooded habitats (landscape corridors), and 97 open habitats (isolating matrix) in Estonia. We defined two species groups of interest: forest (107 species) and corridor specialists (53 species). An extra group of open habitat specialists was extracted for trait scaling. Differing from expectations, forest specialists have high plasticity in reproduction mechanisms: smaller seeds, larger dispersules, complementary selfing ability, and diversity of dispersal vectors. Forest specialists are shorter, less nutrient‐demanding and mycorrhizal‐dependent, stress‐tolerant disturbance‐sensitive competitors, while corridor specialists are large‐seeded disturbance‐tolerant competitors. About 40% of species from local species pools have immigrated into parks. The historic forest area, establishment‐related traits, and stand quality enhance the colonization of forest specialists. The openness of landscape and mowing in the park facilitate corridor specialists. Species traits in parks vary between a forest and corridor specialist, except for earlier flowering and larger propagules. Forest species are not dispersal limited, but they continue to be limited by habitat properties even in the long term. Therefore, the shady parts of historic parks should be appreciated as important forest biodiversity‐enhancing landscape structures. The habitat quality of secondary stands can be improved by nurturing a heterogeneous shrub and tree layer, and modest herb layer management.     

The influence of multi‐scale environmental variables on the distribution of terricolous lichens in a fog desert

Question: How do environmental variables in a hyper‐arid fog desert influence the distribution patterns of terricolous lichens on both macro‐ and micro‐scales? Location: Namib Desert, Namibia. Methods: Sites with varying lichen species cover were sampled for environmental variables on a macro‐scale (elevation, slope degree, aspect, proximity to river channels, and fog deposition) and on a micro‐scale (soil structure and chemistry). Macro‐scale and micro‐scale variables were analysed separately for associations with lichen species cover using constrained ordination (DCCA) and unconstrained ordination (DCA). Explanatory variables that dominated the first two axes of the constrained ordinations were tested against a lichen cover gradient. Results: Elevation and proximity to river channels were the most significant drivers of lichen species cover in the macro‐scale DCCA, but results of the DCA suggest that a considerable percentage of variation in lichen species cover is unexplained by these variables. On a micro‐scale, sediment particle size explained a majority of lichen community variations, followed by soil pH. When both macro and micro‐scale variables were tested along a lichen cover gradient, soil pH was the only variable to show a significant relationship to lichen cover. Conclusion: The findings suggest that landscape variables contribute to variations in lichen species cover, but that stronger links occur between lichen growth and small‐scale variations in soil characteristics, supporting the need for multi‐scale approaches in the management of threatened biological soil crust communities and related ecosystem functions.     

Measuring and comparing the accuracy of species distribution models with presence–absence data

Species distribution models have been widely used to predict species distributions for various purposes, including conservation planning, and climate change impact assessment. The success of these applications relies heavily on the accuracy of the models. Various measures have been proposed to assess the accuracy of the models. Rigorous statistical analysis should be incorporated in model accuracy assessment. However, since relevant information about the statistical properties of accuracy measures is scattered across various disciplines, ecologists find it difficult to select the most appropriate ones for their research. In this paper, we review accuracy measures that are currently used in species distribution modelling (SDM), and introduce additional metrics that have potential applications in SDM. For the commonly used measures (which are also intensively studied by statisticians), including overall accuracy, sensitivity, specificity, kappa, and area and partial area under the ROC curves, promising methods to construct confidence intervals and statistically compare the accuracy between two models are given. For other accuracy measures, methods to estimate standard errors are given, which can be used to construct approximate confidence intervals. We also suggest that as general tools, computer‐intensive methods, especially bootstrap and randomization methods can be used in constructing confidence intervals and statistical tests if suitable analytic methods cannot be found. Usually, these computer‐intensive methods provide robust results.     

Using generalized autoregressive error models to understand fire–vegetation–soil feedbacks in a mulga–spinifex landscape mosaic

Aim To develop a new modelling approach for spatially autocorrelated non‐normal data, and apply it to a case study of the role that fire–vegetation–soil feedbacks play in maintaining boundaries between fire‐sensitive and fire‐promoted plant communities. Location A mulga (Acacia aneura) shrubland–spinifex (Triodia spp.) grassland mosaic, central Australia. Methods Autoregressive error models were extended to non‐normal data by incorporating neighbourhood values of the response and predictor variables into generalized nonlinear models. These models were used to examine the environmental correlates of three response variables: mulga cover; fire frequency in areas free of mulga; and the presence of mulga banding. Mulga cover and mulga banding were assessed visually by overlaying 4477 × 1 km² grid cells on both Landsat 7 ETM+ and very high resolution imagery. Fire frequency was estimated from an existing fire history for central Australia, based on remotely sensed fire scars. Results The autoregressive error models explained 27%, 47% and 57% of the null deviance of mulga cover, fire frequency and mulga banding, respectively, with 12%, 15% and 24% of the null deviance being explained by environmental variables alone. These models accounted for virtually all residual spatial autocorrelation. While there was a clear negative relationship between mulga cover and fire frequency, there was little evidence that mulga was being restricted to parts of the landscape with inherently low fire frequencies. Mulga was most abundant at very low slope angles and on red earths, both of which are likely to reflect high site productivity, while fire frequency was not clearly affected by slope angle and was also relatively high on red earths. Main conclusions The modelling approach we have developed provides a much needed way of analysing spatially autocorrelated non‐normal data and can be easily incorporated into an information‐theoretic modelling framework. Using this approach, we provide evidence that mulga and spinifex have a highly antagonistic relationship. In more productive parts of the landscape, mulga suppresses spinifex and fire, while in less productive parts of the landscape, fire and spinifex suppress mulga, leading to the remarkable abruptness of mulga–spinifex boundaries that are maintained via fire–vegetation–soil feedbacks.     

Signatures of selection in the three‐spined stickleback along a small‐scale brackish water – freshwater transition zone

Local adaptation is often obvious when gene flow is impeded, such as observed at large spatial scales and across strong ecological contrasts. However, it becomes less certain at small scales such as between adjacent populations or across weak ecological contrasts, when gene flow is strong. While studies on genomic adaptation tend to focus on the former, less is known about the genomic targets of natural selection in the latter situation. In this study, we investigate genomic adaptation in populations of the three‐spined stickleback Gasterosteus aculeatus L. across a small‐scale ecological transition with salinities ranging from brackish to fresh. Adaptation to salinity has been repeatedly demonstrated in this species. A genome scan based on 87 microsatellite markers revealed only few signatures of selection, likely owing to the constraints that homogenizing gene flow puts on adaptive divergence. However, the detected loci appear repeatedly as targets of selection in similar studies of genomic adaptation in the three‐spined stickleback. We conclude that the signature of genomic selection in the face of strong gene flow is weak, yet detectable. We argue that the range of studies of genomic divergence should be extended to include more systems characterized by limited geographical and ecological isolation, which is often a realistic setting in nature.     

Predicting effects of large‐scale reforestation on native and exotic birds

Aim

Ecological restoration is critical for recovering biodiversity and ecosystem services, yet designing interventions to achieve particular outcomes remains fraught with challenges. In the extensive regions where non‐native species are firmly established, it is unlikely that historical conditions can be fully reinstated. To what degree, and how rapidly, can human‐dominated areas be shifted via restoration into regimes that benefit target species, communities or processes?

Location

We explore this question in a >20‐year‐old reforestation effort underway at Hakalau Forest National Wildlife Refuge in montane Hawaii. This large‐scale planting of Acacia koa trees is designed to secure populations of globally threatened bird species by transitioning the site rapidly from pasture to native forest.

Methods

We surveyed all forest birds in multiple corridors of young planted trees, remnant corridors of mature trees along gulches and at sites within mature forest. Using a Bayesian hierarchical approach, we identified which factors (distance from forest, habitat type and surrounding tree cover) had the most important influence on native and exotic bird abundance in the reforestation area.

Results

We found that 90% of native and exotic bird species responded quickly, occupying corridors of native trees approximately a decade after planting. However, native and exotic forest birds responded to markedly different characteristics of the reforested area. Native bird abundance was strongly predicted by proximity to mature forest and remnant corridors; conversely, exotic bird abundance was best predicted by overall tree cover throughout the area reforested.

Main conclusions

Our results demonstrate that large‐scale tree planting in corridors adjacent to mature forest can catalyse rapid recovery (both increased abundance and expanded distribution) of forest birds and that it is possible to design reforestation to benefit native species in novel ecosystems.

     

Continental‐scale syntheses of Australian pyromes – misclassification of south‐western eucalypt woodlands misinforms management

Global and continental‐scale analysis of ecological phenomena can offer important insights through the identification of patterns and associations not detectable at smaller scales. However, using proxies for ecological phenomena, such as vegetation mapping for spatially projecting fire regime niches and post‐fire plant responses, require critical examination of predictions to determine utility. Using local studies in south‐western Australia, we demonstrate that while this approach has been largely successful in mallee woodland and shrubland, it has failed in eucalypt woodland, with the consequence that values for a range of fire‐related parameters from the continent‐wide approaches, if adopted in informing management, would result in undesirable conservation outcomes for the world's largest extant temperate woodland.     

Epiphytic lichens on Juniperus communis – an unexplored component of biodiversity in threatened alvar grassland

Semi‐natural grasslands, among them thin‐soil calcareous grasslands (alvars), have great conservation value but have become increasingly rare in Europe. The main threat to alvar grasslands is the encroachment by juniper Juniperus communis and therefore it is usually removed during the restoration practice. Juniper can also be a host plant for many epiphytic lichens, but its role as a phorophyte is poorly known. We studied epiphytic lichen diversity on 126 junipers in 17 sites in western Estonia and found 140 lichenized taxa including several rare and red‐listed species. Using indirect and direct multivariate analyses (DCA, pCCA) and general linear models we revealed that both habitat and phorophyte properties affect lichen assemblies on juniper. Lichen species richness per site showed a unimodal relationship with compound factors of site productivity and juniper characteristics (stem circumference and juniper width). Lichen species richness per phorophyte was increasing with its size and with the proportion of dead branches, and was twice higher in plate alvars than in ryhk alvars. Also, the species composition in plate alvars differed from ryhk alvars by having 42 characteristic lichen species in plate alvars vs three indicators of ryhk alvars. The composition of lichens was significantly influenced by encroachment of alvars, e.g. by high juniper cover and shrub layer height, as well as by the proportion of dead branches and stem circumference of juniper. We conclude that the epiphytic lichen assemblies on junipers are threatened by grassland encroachment similarly to ground layer lichen assemblies. We suggest that some old and scencent junipers should be preserved during the restoration of alvar grasslands.     

Genome‐scale models of metabolism and gene expression extend and refine growth phenotype prediction

Growth is a fundamental process of life. Growth requirements are well‐characterized experimentally for many microbes; however, we lack a unified model for cellular growth. Such a model must be predictive of events at the molecular scale and capable of explaining the high‐level behavior of the cell as a whole. Here, we construct an ME‐Model for Escherichia coli—a genome‐scale model that seamlessly integrates metabolic and gene product expression pathways. The model computes ～80% of the functional proteome (by mass), which is used by the cell to support growth under a given condition. Metabolism and gene expression are interdependent processes that affect and constrain each other. We formalize these constraints and apply the principle of growth optimization to enable the accurate prediction of multi‐scale phenotypes, ranging from coarse‐grained (growth rate, nutrient uptake, by‐product secretion) to fine‐grained (metabolic fluxes, gene expression levels). Our results unify many existing principles developed to describe bacterial growth.     

Characterization of a type of β‐bend ribbon spiral generated by the repeating (Xaa–Yaa–Aib–Pro) motif: The solution structure of harzianin HC IX,a 14‐residue peptaibol forming voltage‐dependent ion channels

The three‐dimensional solution structure of harzianin HC IX, a peptaibol antibiotic isolated from the fungus Trichoderma harzianum, was determined using CD, homonuclear, and heteronuclear two‐dimensional nmr spectroscopy combined with molecular modeling. This 14‐residue peptide, Ac Aib¹ Asn² Leu³ Aib⁴ Pro⁵ Ala⁶ Ile⁷ Aib⁸ Pro⁹ Iva¹⁰ Leu¹¹ Aib¹² Pro¹³ Leuol¹⁴ (Aib, α‐aminoisobutyric acid; Iva, isovaline; Leuol, leucinol), is a main representative of a short‐sequence peptaibol class characterized by an acetylated N‐terminus, a C‐terminal amino alcohol, and the presence of three Aib‐L ‐Pro motifs at positions 4–5, 8–9, and 12–13, separated by two dipeptide units. In spite of a lower number of residues, compared to the 18/20‐residue peptaibols such as alamethicin, harzianin HC IX exhibits remarkable membrane‐perturbing properties. It interacts with phospholipid bilayers, increasing their permeability and forming voltage‐gated ion channels through a mechanism slightly differing from that proposed for alamethicin. Sequence‐specific ¹H‐ and ¹³C‐nmr assignments and conformational nmr parameters (³J_NHCαH coupling constants, quantitative nuclear Overhauser enhancement data, temperature coefficients of amide and carbonyl groups, NH–ND exchange rates) were obtained in methanol solution. Sixty structures were calculated based on 98 interproton distance restraints and 6 Φ dihedral angle restraints, using high temperature restrained molecular dynamics and energy minimization. Thirty‐seven out of the sixty generated structures were consistent with the nmr data and were convergent. The peptide backbone consists in a ribbon of overlapping β‐turns twisted into a continuous spiral from Asn² to Leuol¹⁴ and forming a 26 Å long helix‐like structure. This structure is slightly amphipathic, with the three Aib–Pro motifs aligned on the less hydrophobic face of the spiral where the Asn² side chain is also present, while the more hydrophobic bulky side chains of leucines, isoleucine, isovaline, and leucinol are located on the concave side. The repetitive (Xaa–Yaa–Aib–Pro) tetrapeptide subunit, making up the peptide sequence, is characterized by four sets of (Φ,Ψ) torsional angles, with the following mean values: Φ_i = −90°, Ψ_i = −27°; Φ_i+1 = −98°, Ψ_i+1 = −17°; Φ_i+2 = −49°, Ψ_i+2 = −50°; Φ_i+3 = −78°, Ψ_i+3 = +3°. We term this particular structure, specifically occurring in the case of (Xaa–Yaa–Aib–Pro)_n sequences, the (Xaa–Yaa–Aib–Pro)‐β‐bend ribbon spiral. It is stabilized by 4 → 1 intramolecular hydrogen bonds and differs from both the canonical 3₁₀‐helix made of a succession of type III β‐turns and from the β‐bend ribbon spiral that has been described in the case of (Aib–Pro)n peptide segments. © 1999 John Wiley & Sons, Inc. Biopoly 50: 71–85, 1999