Evaluating the ecological realism of plant species distribution models with ecological indicator values

Species distribution models (SDMs) are routinely applied to assess current as well as future species distributions, for example to assess impacts of future environmental change on biodiversity or to underpin conservation planning. It has been repeatedly emphasized that SDMs should be evaluated based not only on their goodness of fit to the data, but also on the realism of the modeled ecological responses. However, possibilities for the latter are hampered by limited knowledge on the true responses as well as a lack of quantitative evaluation methods. Here we compared modeled niche optima obtained from European-scale SDMs of 1476 terrestrial vascular plant species with empirical ecological indicator values indicating the preferences of plant species for key environmental conditions. For each plant species we first fitted an ensemble SDM including three modeling techniques (GLM, GAM and BRT) and extracted niche optima for climate, soil, land use and nitrogen deposition variables with a large explanatory power for the occurrence of that species. We then compared these SDM-derived niche optima with the ecological indicator values by means of bivariate correlation analysis. We found weak to moderate correlations in the expected direction between the SDM-derived niche optima and ecological indicator values. The strongest correlation occurred between the modeled optima for growing degree days and the ecological indicator values for temperature. Correlations were weaker for SDM-derived niche optima with a more distal relationship to ecological indicator values (notably precipitation and soil moisture). Further, correlations were consistently highest for BRT, followed by GLM and GAM. Our method gives insight into the ecological realism of modeled niche optima and projected core habitats and can be used to improve SDMs by making a more informed selection of environmental variables and modeling techniques.     

Multiple pH and temperature optimum of extracellular xylanase from Trichoderma reesei QM 9414

The rate of total extracellular xylanase production in Trichoderma reesei, QM 9414, system was affected by temperature and pH. In vitro studies with xylanase showed different temperature optima for activity in presence and in absence of xylan as substrate. Similar behaviour was observed in the pH studies. A number of temperature and pH optima also suggested the multiple nature of xyalanase.     

The temperature optima of enzymes: a new perspective on an old phenomenon

Careful analysis of the dependence of enzyme activity on assay temperature has revealed that some enzymes might have real temperature optima in which the decrease in catalytic rate at temperatures above the optimum is not primarily a result of irreversible thermal inactivation. The 'equilibrium model' has been formulated to describe genuine temperature optima, and to suggest a simple experimental method by which to distinguish these cases from those in which enzyme instability is the major determinant of temperature optima.     

The effect of pH on chemiluminescence of different probes exposed to superoxide and singlet oxygen generators

The compromised optima for high intensity chemiluminescence (CL), using superoxide generators, were all above pH 9.0 for the CL probes luminol and lucigenin. With luminol the optima were at pH 9.0 and 9.4 for the generators KO₂ and hypoxanthine/xanthine oxidase (HX/XO), respectively. Lucigenin, with the same generators, produced optima at pH 9.5 and 10.0, respectively. The probe methyl-Cypridina-luciferin analogue (MCLA) produced optima closer to neutral pH, which is preferred for physiological assessments. MCLA had optima at pH 6.0, 8.7 and 9.5 with KO₂ and with HX/XO optima at pH 4.8, 6.0, 7.0 and 8.7. When CL was assessed at physiological pH, MCLA observed superoxide radicals with a sensitivity of 100- and 330-fold more than luminol or luicigenin respectively. For singlet oxygen, the sensitivity of MCLA at this pH was 45- and 5465-fold more than for the said probes respectively. H₂O₂ did not elicit CL between pH 4 and 9.5 with any of the probes and did not influence the production of superoxide or singlet oxygen when co-assessed. Therefore CL could only be obtained when enzymes were used as converters. The optima for the enzyme-conversion system horseradish peroxidase (HRP)/H₂O₂, and luminol, were at pH 8.0 and 9.2. Lucigenin and HRP/H₂O₂ also had a biphasic CL profile with optima at pH 7.4 and 9.6. MCLA and HRP/H₂O₂ had five optima, with the major ones at pH 6.1 and beyond 10. The optima for the myeloperoxidase/H₂O system were at 8.6 and beyond 10.0 when luminol and 0.15 mol/L NaBr were used. © 1997 John Wiley & Sons, Ltd.     

Invertase and maltase in the free space of the maize scutellum

When maize scutellum slices were incubated in solutions of sucrose or maltose, there was a release of glucose into the bathing solution. The pH optima for glucose release were 2.5 for sucrose and 3.5 for maltose. From measurement of rates of glucose uptake into slices in the presence or absence of sucrose, it is calculated that glucose uptake will introduce errors of 3–9%, depending on the sucrose concentration, in estimates of free-space sucrose-hydrolase activity at pH 2.5. At their respective pH optima, maltose was hydrolysed at a rate 2.5 times that of sucrose. When frozen-thawed slices were used the same pH optima were obtained, but rates of hydrolysis were increased. Raffinose and melezitose also were hydrolysed with pH optima of 2.5 and 3.5, respectively. α-Methyl glucose was not hydrolysed. A 60-min HCl treatment (pH 2) of scutellum slices destroyed 69% of the sucrose-hydrolase activity and 100% of the maltose-hydrolase activity. In contrast, sucrose uptake and sucrose synthesis from exogenous fructose were not affected by HCl treatment. It is concluded that there are two hydrolases, acid invertase and maltase; that they are either on or outside the plasmalemma (in the free space); and that they are not necessary to the disaccharide uptake processes either by supplying exogenous hexose or by acting as transporters.     

Temperature compensation of [u-C]glucose incorporation by microbial communities in a river with a fluctuating thermal regime

In summer, the river Saar in the southwest of Germany exhibits distinct temperature fluctuations from 8 degrees C at the source to nearly 30 degrees C in the middle region. Temperature optima for bacterial plate counts and the uptake velocity of [U-C]glucose by the natural microbial communities of different regions ranged from 20 to 30 degrees C, which is significantly above the mean annual water temperature. A correlation between temperature optima and different seasons or habitats was not observed. Despite the relatively high temperature optima, the turnover time for glucose was shortest at temperatures around the mean annual water temperature, due to changes in the substrate affinity. At limiting substrate concentrations, the higher substrate affinity at lower temperatures may lead to a higher real activity at in situ temperatures, and a compensatory stabilization of uptake rates at fluctuating temperatures is possible.     

Kinetic and thermodynamic properties of an immobilized glucoamylase from a mesophilic fungus, Arachniotus citrinus

Purified glucoamylase from Arachniotus citrinus was immobilized on polyacrylamide gel with 70% yield of immobilization. The immobilization improved the pH optima, temperature optima, values of K(m), V(max), and activation energy. Irreversible thermal denaturation studies of soluble and immobilized glucoamylase indicated that immobilization decreased the entropy and enthalpy of deactivation by magnitudes and made the immobilized glucoamylase thermodynamically more stable.     

Effect of pH on Anaerobic Mild Steel Corrosion by Methanogenic Bacteria

Methanogens can use H₂ produced by cathodic depolarization-mediated oxidation of elemental iron to produce methane. Thermodynamic consideration of the cathodic depolarization mechanism predicts more oxidation of Fe⁰ at lower pH. Methanogenic responses to pH by Methanococcus deltae, Methanococcus thermolithotrophicus, and Methanosarcina barkeri were examined. When grown on H₂-CO₂, these bacteria had pH optima from 6.2 to 7.0, but when all H₂ was supplied from Fe⁰, methanogenic pH optima were lower, 5.4 to 6.5. Corrosion was monitored with and without cultures and at various pHs; more corrosion occurred when cultures were present, biologically induced corrosion was greatest at the pH optima for methanogenesis from Fe⁰, and corrosion without cultures increased with a drop in pH.     

Optimum walking techniques for idealized animals

The vertical component of the force exerted by a foot on the ground, in the course of a step, may rise to a single maximum and decline again (as in human running) or may show two distinct maxima (as in human walking). A foot may remain on the ground for a large or small fraction of the duration of a stride. Mathematical models are used to investigate the effects of these differences of technique on the energy cost of locomotion. The optimum technique for a biped at a given speed is different from the optimum for a hypothetical many-legged animal. The optima for quadrupedal walking are likely to lie between these extremes.
The walking techniques adopted by men at different speeds are close to the optima indicated by the bipedal model. The two maxima of the force exerted by a foot are higher, and have a lower minimum between them, at higher speeds of walking. The techniques adopted by a sheep are close to the optima indicated by the many-legged model but dogs use techniques rather closer to the optima for bipeds.
The limitations of the models are discussed.     

Temperature Compensation of [U-14C]Glucose Incorporation by Microbial Communities in a River with a Fluctuating Thermal Regime

In summer, the river Saar in the southwest of Germany exhibits distinct temperature fluctuations from 8°C at the source to nearly 30°C in the middle region. Temperature optima for bacterial plate counts and the uptake velocity of [U-¹⁴C]glucose by the natural microbial communities of different regions ranged from 20 to 30°C, which is significantly above the mean annual water temperature. A correlation between temperature optima and different seasons or habitats was not observed. Despite the relatively high temperature optima, the turnover time for glucose was shortest at temperatures around the mean annual water temperature, due to changes in the substrate affinity. At limiting substrate concentrations, the higher substrate affinity at lower temperatures may lead to a higher real activity at in situ temperatures, and a compensatory stabilization of uptake rates at fluctuating temperatures is possible.     

Simplex‐based optimization of numerical and categorical inputs in early bioprocess development: Case studies in HT chromatography

Bioprocess development studies often involve the investigation of numerical and categorical inputs via the adoption of Design of Experiments (DoE) techniques. An attractive alternative is the deployment of a grid compatible Simplex variant which has been shown to yield optima rapidly and consistently. In this work, the method is combined with dummy variables and it is deployed in three case studies wherein spaces are comprised of both categorical and numerical inputs, a situation intractable by traditional Simplex methods. The first study employs in silico data and lays out the dummy variable methodology. The latter two employ experimental data from chromatography based studies performed with the filter‐plate and miniature column High Throughput (HT) techniques. The solute of interest in the former case study was a monoclonal antibody whereas the latter dealt with the separation of a binary system of model proteins. The implemented approach prevented the stranding of the Simplex method at local optima, due to the arbitrary handling of the categorical inputs, and allowed for the concurrent optimization of numerical and categorical, multilevel and/or dichotomous, inputs. The deployment of the Simplex method, combined with dummy variables, was therefore entirely successful in identifying and characterizing global optima in all three case studies. The Simplex‐based method was further shown to be of equivalent efficiency to a DoE‐based approach, represented here by D‐Optimal designs. Such an approach failed, however, to both capture trends and identify optima, and led to poor operating conditions. It is suggested that the Simplex‐variant is suited to development activities involving numerical and categorical inputs in early bioprocess development.     

Thermal biology of mosquito‐borne disease

Mosquito‐borne diseases cause a major burden of disease worldwide. The vital rates of these ectothermic vectors and parasites respond strongly and nonlinearly to temperature and therefore to climate change. Here, we review how trait‐based approaches can synthesise and mechanistically predict the temperature dependence of transmission across vectors, pathogens, and environments. We present 11 pathogens transmitted by 15 different mosquito species – including globally important diseases like malaria, dengue, and Zika – synthesised from previously published studies. Transmission varied strongly and unimodally with temperature, peaking at 23–29ºC and declining to zero below 9–23ºC and above 32–38ºC. Different traits restricted transmission at low versus high temperatures, and temperature effects on transmission varied by both mosquito and parasite species. Temperate pathogens exhibit broader thermal ranges and cooler thermal minima and optima than tropical pathogens. Among tropical pathogens, malaria and Ross River virus had lower thermal optima (25–26ºC) while dengue and Zika viruses had the highest (29ºC) thermal optima. We expect warming to increase transmission below thermal optima but decrease transmission above optima. Key directions for future work include linking mechanistic models to field transmission, combining temperature effects with control measures, incorporating trait variation and temperature variation, and investigating climate adaptation and migration.     

The causes of variation in tree seedling traits: the roles of environmental selection versus chance

A key aspect of biodiversity is the great quantitative variation in functional traits observed among species. One perspective asserts that trait values should converge on a single optimum value in a particular selective environment, and consequently trait variation would reflect differences in selective environment, and evolutionary outcomes would be predictable. An alternative perspective asserts that there are likely multiple alternative optima within a particular selective environment, and consequently different lineages would evolve toward different optima due to chance. Because there is evidence for both of these perspectives, there is a long-standing controversy over the relative importance of convergence due to environmental selection versus divergence due to chance in shaping trait variation. Here, I use a model of tree seedling growth and survival to distinguish trait variation associated with multiple alternative optima from variation associated with environmental differences. I show that variation in whole plant traits is best explained by environmental differences, whereas in organ level traits variation is more affected by alternative optima. Consequently, I predict that in nature variation in organ level traits is most closely related to phylogeny, whereas variation in whole plant traits is most closely related to ecology.     

Ellenberg’s water table experiment put to the test: species optima along a hydrological gradient

An important aspect of niche theory is the position of species’ optima along ecological gradients. It is widely believed that a species’ ecological optimum takes its shape only under competitive pressure. The ecological optimum, therefore, is thought to differ from the physiological optimum in the absence of interspecific competition. Ellenberg’s Hohenheim water table experiment has been very influential in this context. However, the water table gradient in Ellenberg’s experiment was produced by varying the soil thickness above the water table, which confounded the potentially disparate impacts of water table depth (WTD) and soil depth on species growth. Accordingly, here we have re-evaluated Ellenberg’s work. Specifically, we tested the hypothesis that physiological and ecological optima are identical and unaffected by interspecific interaction. We used the same six grasses as in Ellenberg’s experiments, but in our mesocosms, WTD was varied but soil depth kept constant. The design included both an additive component (with/without plant interaction) and a substitutive component (monocultures vs. species mixtures). The results show that the physiological optima along the hydrological gradient varied greatly between species, even in the absence of interspecific interaction. Within species, however, physiological and ecological optima appeared identical in most cases, irrespective of the competition treatment. We conclude that the ‘physiological capacity’ of species largely determines where they are able to persist and that any impact of interspecific interaction is only marginal. These findings are at variance with Ellenberg’s rule, where competition is considered to shift the distribution of a species away from its physiological optimum.     

Purification and characterization of a thermostable glucoamylase from a Myrothecium isolate

Two glucoamylases, gluc I and gluc II, were purified to homogeneity from the culture filtrate of a Myrothecium strain M1 by chromatography on DEAE-cellulose and concanavalin A-sepharose. Molecular masses deduced by SDS-PAGE were 72000 ± 2500 for gluc I and 96 000 ± 4000 for glue II. The temperature optima of the enzymes were both about 70°C and their pH optima were around 4.0. Both enzymes were glycoprotein and preferentially hydrolysed high molecular mass substrates. Hg²⁺ was a potent inhibitor of both glucoamylases. Glue II had higher debranching activity than gluc I.     

Multiple maxima of likelihood in phylogenetic trees: an analytic approach

Maximum likelihood (ML) is a widely used criterion for selecting optimal evolutionary trees. However, the nature of the likelihood surface for trees is still not sufficiently understood, especially with regard to the frequency of multiple optima. Here, we initiate an analytic study for identifying sequences that generate multiple optima. We concentrate on the problem of optimizing edge weights for a given tree or trees (as opposed to searching through the space of all trees). We report a new approach to computing ML directly, which we have used to find large families of sequences that have multiple optima, including sequences with a continuum of optimal points. Such data sets are best supported by different (two or more) phylogenies that vary significantly in their timings of evolutionary events. Some standard biological processes can lead to data with multiple optima, and consequently the field needs further investigation. Our results imply that hill-climbing techniques as currently implemented in various software packages cannot guarantee that one will find the global ML point, even if it is unique.     

Purification of alpha-amylase isoenzymes from Scytalidium thermophilum on a fluidized bed of alginate beads followed by concanavalin A-agarose column chromatography

An alpha-amylase has been purified from the thermophilic fungus Scytalidium thermophilum. A ninefold purification was achieved in a single step using fluidized bed chromatography wherein alginate was used as the affinity matrix. There are at least two isoenzymes as shown by concanavalin A (Con A)-agarose column chromatography. The isoenzyme binding to Con A is stable for at least 3 h at 80 degrees C in the presence of calcium ions. The isoenzymes have similar molecular weights of around 45,000 Da as shown by SDS-PAGE analysis. The isoenzymes differ only slightly in their pH optima and temperature optima but the isoenzyme binding to Con A-agarose has slightly higher thermal stability.     

Use and improvement of Ellenberg's indicator values in deciduous forests of the Boreo-nemoral zone in Sweden

Ellenberg's indicator values for light, moisture and reaction were tested in deciduous hardwood forests of the Boreo-nemoral zone m Sweden Weighted averages of indicator values were calculated and correlated with field measurements for two test sets of relevés The best, highly significant correlations were found for reaction, particularly for weighted averages based on vascular plant species Significant correlations were also found for light, whereas those for moisture were less good and only partly significant Weighted averages based on presence/absence values and those based on cover/abundance values were generally very similar to each other, but showed differences in their correlations with actual measurements
A training set of relevés was used to calculate optima and ecological amplitudes of the most common species Under certain conditions, the original indicator values were replaced by these optima in order to obtain improved indicator values for Swedish deciduous forests These were correlated with the same test sets of field measurements as the original values and clearly gave better results for light as well as for reaction regarding vascular plants No clear differences were found for moisture and reaction regarding bryophytes For the majority of species, the original indicator values also expressed the ecological optima in Swedish deciduous forests as determined by this study However, several species, most of them preferring more open habitats, showed ecological optima and amplitudes that considerably deviated from central European conditions In conclusion, Ellenberg's indicator values can successfully be used in south Swedish deciduous forests, particularly after calibration of the values according to regional deviations     

Properties of peroxidases from tobacco cell suspension culture

An enzyme preparation from suspension cultured tobacco cells oxidized IAA only in the presence of added cofactors, Mn²⁺ and 2,4-dichlorophenol, and showed two pH optima for the oxidation at pH 4·5 and 5·5. Effects of various phenolic compounds and metal ions on IAA oxidase activity were examined. The properties of seven peroxidase fractions separated by column chromatography on DEAE-cellulose and CM-Sephadex, were compared. The peroxidases were different in relative activity toward o-dianisidine and guaiacol. All the peroxidases catalysed IAA oxidation in the presence of added cofactors. The pH optima for guaiacol peroxidation were very similar among the seven isozymes, but the optima for IAA oxidation were different. The anionic and neutral fractions showed pH optima near pH 5·5, but the cationic isozymes showed optima near pH 4·5. With guaiacol as hydrogen donor, an anionic peroxidase (A-1) and a cationic peroxidase (C-4) were very different in H₂O₂ concentration requirements for their activity. Peroxidase A-1 was active at a wide range of H₂O₂ concentrations, while peroxidase C-4 showed a more restricted H₂O₂ requirement. Gel filtration and polyacrylamide gel studies indicated that the three cationic peroxidases have the same molecular weight.     

Studies on the biosynthesis of gramicidin S in a cell-free system from Bacillus brevis. Further attempts to elucidate its mechanism of synthesis

1. The pH optima for the incorporation of (14)C-labelled amino acids into gramicidin S by an 11000g cell-free extract from Bacillus brevis have been determined. The pH optima for leucine, proline, phenylalanine, ornithine and valine were 7.5-7.7, 7.5-7.7, 7.7-7.9, 7.7-7.9 and 8.0-8.2 respectively. Hence the greatest difference in pH optima existed between leucine and valine, where it was 0.5pH unit. 2. The 11000g cell-free extract incorporated into gramicidin S only the l-isomers of valine, proline and ornithine. However, both isomers of leucine are utilized and the experiments indicate that a leucine racemase exists in the 11000g cell-free extract. With phenylalanine the l-isomer is utilized much more effectively than the d-isomer. This is noteworthy since it is the d-isomer that occurs in gramicidin S. The experiments indicate that conversion of the l-isomer into the d-form takes place at a stage beyond that of the free amino acid.