Ecosystemic structural–functional approach of the state and transition model

Objective: To contribute to the integration of key ecological concepts such as dynamic equilibrium, critical threshold, resistance and resilience to the ‘State and Transition Model’ (STM), in order to apply them in a more feasible way for rangeland management. Methods: Review and discussion of conceptual models and applied literature, including examples of rangeland dynamics. Results and Conclusions: We propose to enhance the STM considering two principal axes: (a) the x axis determined by structural ecosystem changes (vegetation and soil) and (b) the y axis determined by ecosystem functions and/or processes (recruitment, rain use efficiency). These axes define what we will call Structural–Functional State and Transition Model (SFSTM). Both axes of SFSTM make it possible to determine and quantify states and transitions, critical thresholds and to evaluate the resistance and resilience of an ecosystem to a given disturbance. The critical threshold is identified by structural and functional thresholds (x and y axes), thus defining the point where the ecosystem loses its resilience. Furthermore, in the supplementary file we provide examples with field data from Patagonia to illustrate the SFSTM. The proposed SFSTM has large implications for rangeland research and management, facilitating the understanding and integration of key concepts to enhance the STM. The identification of variables to assess structure and processes makes the model more useful.     

Grassland responses to multiple disturbances on the New England Tablelands in NSW,Australia

Disturbances have played a significant role in shaping vegetation patterns following European settlement and agricultural development in Australia, particularly over the last 100 years. However, little is known about the temporal dynamics of plant communities in relation to disturbances and their interactions. In this study we examined the response and recovery of temperate grassland communities to disturbance, using a multi-factorial experiment involving grazing exclusion (absent and present), fire (absent and present), soil cultivation (none, 5 and 20 cm) and soil amendment (none, fertiliser and fertiliser plus clover seeds) on the New England Tablelands in NSW, Australia. Temporal patterns of plant communities were analysed using detrended correspondence analysis for eight surveys over 24 months. Vegetation patterns at each survey were analysed using principal components analysis. The effects of treatments on malleability (Bray–Curtis dissimilarity) of plant communities were analysed using a linear mixed model, and the relationships between malleability and plant species groups were depicted using a generalised additive model and further analysed using a linear model. Perennial native grasses and a non-native forb (Hypochaeris radicata) initially dominated the vegetation, but after the disturbances H. radicata and other non-native species dominated. Compositional changes from the initial states were greatest in the first spring (7 months after treatment application), and then the vegetation tended to recover towards its original state. Soil cultivation resulted in the greatest deviation in community composition, followed by soil amendment, fire, with grazing exclusion the least. The recovery process and rate of recovery varied with treatment reflecting the dominance of soil cultivation and its interactions with other forms of disturbances. Soil amendment and grazing exclusion tended to reduce the effects of soil cultivation. Malleability was negatively related to perennial native grasses; positively to other non-native species, annual native grasses and perennial native sedges/rushes; and negatively to H. radicata when its cover was below 18%, but positively when above 18%. The degree of malleability reflected the high resilience of the vegetation to disturbance, and was mainly due to the recovery of perennial native grasses and H. radicata. This resilience demonstrated that the small-scale disturbances did not cause vegetation to cross an ecological threshold and that the present vegetation is resilient to common disturbances occurring at small scales. The results also suggest (1) that the present vegetation has developed mechanisms to adapt to these disturbances, (2) the importance of disturbance scale or (3) that the ecological threshold had already been crossed and the present vegetation is in a degraded state compared with its original state before the end of the 19th century.     

A hierarchical deductive approach for functional types in disturbed ecosystems

Abstract. We propose a hierarchical approach for plant functional classification in disturbed ecosystems to be used for vegetation modelling and global plant trait comparisons. Our framework is based on the persistence of plants at different levels of organization. We assume that the main parameters to determine persistence in chronically disturbed ecosystems are those related to: I ndividual‐persistence capacity, P ropagule‐persistence capacity (persistence at the population level), C ompetitive capacity (persistence at the community level) and D ispersal capacity (persistence at the landscape level). The IPCD approach is illustrated for fire‐prone and grazed ecosystems from the Mediterranean region and Australia and by assuming a binary classification of the four traits determining persistence which give a total 16 possible functional types. The IPCD framework provides a simple structured and synthetic view from which more elaborated schemes can be developed.     

A model of the transition state in the alkaline phosphatase reaction

A high resolution crystal structure of Escherichia coli alkaline phosphatase in the presence of vanadate has been refined to 1.9 A resolution. The vanadate ion takes on a trigonal bipyramidal geometry and is covalently bound by the active site serine nucleophile. A coordinated water molecule occupies the axial position opposite the serine nucleophile, whereas the equatorial oxygen atoms of the vanadate ion are stabilized by interactions with both Arg-166 and the zinc metal ions of the active site. This structural complex supports the in-line displacement mechanism of phosphomonoester hydrolysis by alkaline phosphatase and provides a model for the proposed transition state in the enzyme-catalyzed reaction.     

Anthropogenic impact of mercury accumulation in fish from the Rio Madeira and Rio Negro rivers (Amazonia)

Fish is an important concentrator of mono-methyl mercury and the main route to human contamination. We compared fish Hg bioaccumulation (within similar weight ranges) in two Amazonian river habitats during high-water seasons. The Rio Madeira has been greatly impacted by agriculture, alluvial gold extraction, and a hydroelectric reservoir, whereas the Rio Negro is much less affected by these human activities. The species at the top of the food web, Hoplias malabaricus (piscivorous; 80-668 ng Hg/g) and Cichla spp. (piscivorous; 42–747 ng Hg/g) showed the highest range of Hg concentrations. Nonpiscivorous species with comparable weight range, such as Potamorhina latior (detritivorous; 20–157 ng Hg/g) and Myleus torquatus (herbivorous; 2–182 ng Hg/g), had lower Hg concentrations. Triportheus elongatus (omnivorous; 5–350 ng Hg/g), with the lowest weight range, also showed a low range of Hg concentrations. Despite the Rio Madeira's higher sediment load as well as environmental impacts (deforestation, agriculture, hydroelectric reservoir, and alluvial gold mining) on natural Hg release, fish Hg bioaccumulation was no different between the two river habitats for nonpiscivorous species. In this small observational study only the species at the top of the food web (M. torquatus, Cichla spp, T. elongatus) showed higher mean Hg concentrations in the Rio Madeira than the dominantly wilderness habitat of the Rio Negro.     

Hematological parameters of three freshwater stingray species (Chondrichthyes: Potamotrygonidae) in the middle Rio Negro,Amazonas state

This paper aimed to study and compare the hematology of newborns, young, subadults, adult males, adult females and pregnant females of Potamotrygon wallacei (cururu stingray), Potamotrygon motoro and Paratrygon aiereba. Newborn cururu stingrays had lower red blood parameters than those of other development stages. Thrombograms and leukograms showed a conservative pattern between development stage, sexual dimorphism and pregnancy. In P. motoro and P. aiereba, variables relating to red blood parameters, biochemistry and leukograms showed little variation between the species' biological characteristics, thus showing that these variables are not good criteria for differentiating them within the same species. In conclusion, the development stage is an important factor for differentiating hematological properties in the cururu stingray, while this has not been observed in P. motoro and P. aiereba stingrays.     

A new Apistogramma species (Teleostei, Cichlidae) from the Rio Negro in Brazil and Venezuela

Apistogramma diplotaenia sp.n. occurs in the upper and middle Rio Negro. The largest among 186 specimens studied is a 29.2 mm SL male, the largest female is 22.9 mm SL. Distinguishing characters include a unique colour pattern, consisting of two dark bands along the side which converge anteriorly and posteriorly. A comparative osteological study, including other species of Apistogramma and the genera Taeniacara and Apistogrammoides , indicates a progressive forwards loss of infraorbital ossicles and foramina among dwarf cichlids. The long, rod-like interarcual cartilage of Apistogramma, Apistogrammoides and Satanoperca possibly represents a plesiomorphic condition otherwise unknown among cichlids.     

Change in the vegetation mosaic of central Arizona USA between 1940 and 1989

The landscape of central Arizona U.S.A. is characterized by a patchy distribution of three major vegetation types: chaparral, woodland and grassland. Disturbance is common in the landscape, primarily livestock grazing, fire and conversion (i.e., removal of woody plants to increase forage for livestock). The purposes of this research were to determine changes in the landscape mosaic of central Arizona between 1940 and 1989 and to predict future changes. Using aerial photographs from 1940, 1968 and 1989 and digital overlays followed by transition matrix analysis, we found that chaparral and its adjacent grassland had changed less than woodland and its grassland. However, both had nearly equal projected stabilization times. Moreover, disturbance increased time for stabilization and some results were scale-dependent.     

Post-fire and post-quarry rehabilitation successions in Mediterranean-like ecosystems: Implications for ecological restoration

Resilience against sudden changes in the environment is a very desirable trait in plants used for ecosystem restoration. Mediterranean-like vegetation exhibits particularly strong fire resilience. There are two main functional groups of fire-prone species among Mediterranean-like vegetation: seeders and resprouters. Our aims were to describe how the theory of succession after fire relates to rehabilitation and to use this knowledge to improve the results of rehabilitation attempts in Mediterranean-like ecosystems. Eight post-fire (PF) sites, 14 post-rehabilitated (PR) quarry sites and two woodland sites were sampled. Detrended Canonical Correspondence Analysis (DCCA) showed that PF and PR successions were quite different. Both displayed an increasing abundance of resprouters over time, but seeder density increased throughout PR succession and decreased during PF succession. Nine species were common to both successions in all studied stages. The results showed that until 15-21 years of succession, the post-rehabilitation sites had not become as resilient to fires as sites populated by indigenous vegetation due to the lack of a seeder seed bank. However, after 21 years of PR succession, the exponentially increasing seeder population may allow for seed bank formation and thus eventually improve the fire resilience of the site.     

A simple model for the dynamics of a host-parasite-hyperparasite interaction

Hyperparasites can play a crucial role in the control of a host-parasite interaction if they are successfully established in the community. We investigated the specific traits of the hyperparasite and those of the release event which allow a successful regulation of primary parasite populations. This study has been motivated by the case study of chestnut-Cryphonectria parasitica-Cryphonectria Hypovirus interaction. We use a model of SIR/SIS type which assumes a limited diffusion of the parasite. Our model emphasizes the thresholds for invasion linked to the ecological specificities of both the pathogen and the hyperparasite (transmission rates and virulence) and to the initial conditions of the system (population sizes of the different categories). The predictions are consistent with data on the observed spread of the virus. "Mild" strains of the hyperparasite, characterized by a high vertical transmission rate and low virulence, are more prone to establish than "severe" strains. It also demonstrates that the horizontal transmission of the virus, which is controlled by a vegetative incompatibility system in the fungus, is not the unique constraint for the virus establishment. This study may contribute to theoretical and practical aspects of the biological control of plant diseases with a hyperparasite and to the ecology of biological invasions.     

Electrostatic interactions in the denatured state and in the transition state for protein folding: effects of denatured state interactions on the analysis of transition state structure

The development of electrostatic interactions during the folding of the N-terminal domain of the ribosomal protein L9 (NTL9) is investigated by pH-dependent rate equilibrium free energy relationships. We show that Asp8, among six acidic residues, is involved in non-native, electrostatic interactions with K12 in the transition state for folding as well as in the denatured state. The perturbed native state pK(a) of D8 (pK(a) = 3.0) appears to be maintained through non-native interactions in both the transition state and the denatured state. Mutational effects on the stability of the transition state for protein (un)folding are often analyzed in respect to change in ground states. Thus, the interpretation of transition state analysis critically depends on an understanding of mutational effects on both the native and denatured state. Increasing evidence for structurally biased denatured states under physiological conditions raises concerns about possible denatured state effects on folding studies. We show that the structural interpretation of transition state analysis can be altered dramatically by denatured state effects.     

Regulation of the distribution of chlorophyll and phycobilin-absorbed excitation energy in cyanobacteria. A structure-based model for the light state transition

The light state transition regulates the distribution of absorbed excitation energy between the two photosystems (PSs) of photosynthesis under varying environmental conditions and/or metabolic demands. In cyanobacteria, there is evidence for the redistribution of energy absorbed by both chlorophyll (Chl) and by phycobilin pigments, and proposed mechanisms differ in the relative involvement of the two pigment types. We assayed changes in the distribution of excitation energy with 77K fluorescence emission spectroscopy determined for excitation of Chl and phycobilin pigments, in both wild-type and state transition-impaired mutant strains of Synechococcus sp. PCC 7002 and Synechocystis sp. PCC 6803. Action spectra for the redistribution of both Chl and phycobilin pigments were very similar in both wild-type cyanobacteria. Both state transition-impaired mutants showed no redistribution of phycobilin-absorbed excitation energy, but retained changes in Chl-absorbed excitation. Action spectra for the Chl-absorbed changes in excitation in the two mutants were similar to each other and to those observed in the two wild types. Our data show that the redistribution of excitation energy absorbed by Chl is independent of the redistribution of excitation energy absorbed by phycobilin pigments and that both changes are triggered by the same environmental light conditions. We present a model for the state transition in cyanobacteria based on the x-ray structures of PSII, PSI, and allophycocyanin consistent with these results.     

Modeling the hazard of transition into the absorbing state in the illness-death model

The illness-death model is the simplest multistate model where the transition from the initial state 0 to the absorbing state 2 may involve an intermediate state 1 (e.g., disease relapse). The impact of the transition into state 1 on the subsequent transition hazard to state 2 enables insight to be gained into the disease evolution. The standard approach of analysis is modeling the transition hazards from 0 to 2 and from 1 to 2, including time to illness as a time-varying covariate and measuring time from origin even after transition into state 1. The hazard from 1 to 2 can be also modeled separately using only patients in state 1, measuring time from illness and including time to illness as a fixed covariate. A recently proposed approach is a model where time after the transition into state 1 is measured in both scales and time to illness is included as a time-varying covariate. Another possibility is a model where time after transition into state 1 is measured only from illness and time to illness is included as a fixed covariate. Through theoretical reasoning and simulation protocols, we discuss the use of these models and we develop a practical strategy aiming to (a) validate the properties of the illness-death process, (b) estimate the impact of time to illness on the hazard from state 1 to 2, and (c) quantify the impact that the transition into state 1 has on the hazard of the absorbing state. The strategy is also applied to a literature dataset on diabetes.     

Linking small desert mammal distribution to habitat structure in a protected and grazed landscape of the Monte, Argentina

Interpretation of landscape patterns from the perspective of different species allows knowing the way in which they perceive landscape, and how their perception varies with scale. We examined distribution of four small mammal species at different scales over a landscape including protected and grazed areas, and associated species distribution with landscape structure. The study was conducted in the central Monte Desert (Reserve of Ñacuñán). Trap grids were set in both areas at two scales, varying their grain and extent. To determine whether spatial patterns are random, clumped or regular, we used a point pattern analysis. Logistic regressions were performed to relate the presence-absence of small mammals to environmental variables. Intensity of the point pattern was not constant, either in the Reserve or the grazed area. Small mammal abundance exhibited a heterogeneous distribution, and the existence of a first-order effect was detected for all species. No second-order effects were detected, the point pattern was random for all species in both areas. Both areas were differently perceived by rodent species. Habitat structure in both conditions and its variations with scale appear to be important factors affecting distribution patterns.     

Temporal and micro-spatial patterning of seedling establishment. Consequences for patch dynamics in the southern Monte,Argentina

We compared the temporal and micro-spatial patterning of seedling emergence and establishment of two cohorts of perennial grasses and shrubs in the southern Monte, Argentina. Samplings were carried out in two contrasting areas (grazed and non-grazed) during four years. We found lower densities of emerged and established seedlings of perennial grasses in the grazed relative to the non-grazed area. Conversely, emerged seedlings of shrubs did not vary between the grazed and the non-grazed area and densities of established shrub seedlings were higher in the grazed than in the non-grazed area. We only found differences between cohorts in seedling emergence of perennial grasses. These differences could be associated with the amount of precipitation in the year previous to the emergence. Both in the grazed and non-grazed area, seedlings of perennial grasses were concentrated at the periphery of plant patches. We defined a plant patch as a discrete unit of the spatial pattern of vegetation surrounded by, at least, 20 cm of bare soil from the nearest neighbour patch. Emergence in perennial grasses was more frequent at the southern/western patch-periphery than at other patch-periphery locations. Established seedlings of perennial grasses, however, were homogeneously distributed throughout patch periphery. Emergence in shrubs was more frequent at the centre and periphery of patches than at inter-patch microsites. In contrast, established seedlings of shrubs were homogeneously distributed among microsites. Our results suggests that differential seedling establishment between life forms is the outcome of complex biotic and abiotic interactions and feedbacks at the patch level between seedlings and established plants. Both life forms appear to have a different role in the origin, dynamics, and maintenance of spotting vegetation. Because of the ability to establish both at inter-patch and patch microsites, shrubs could be identified as colonizers or initiators of small plant patches in bare soil or they may contribute to increase the cover and size of pre-existing plant patches. Both processes would be promoted in grazed areas. Due to the ability to establish at patch peripheries, perennial grasses would contribute to the isodiametric growth of pre-existing patches, preferentially in non-grazed areas. This revised version was published online in June 2006 with corrections to the Cover Date.     

Phosphorus and nitrogen status in soils and vegetation along a toposequence of dystrophic rainforests on the upper Rio Negro

Amazon forests along a toposequence at San Carlos de Rio Negro (Venezuela) show distinct nutrient limitations depending on slope position. Soils were collected by genetic horizons and analysed to provide information on the relationships between soil P and N status and the nutrition of natural forest at three locations along the toposequence. The upper-slope tierra firme sites had total P concentrations between 100 and 200 g g^–1 in the mineral soil fines and between 700 and 1100 g g^–1 in lateritic nodules. Hyphae were seen to explore lateritic nodules and may contribute to P nutrition. Total P in the mineral soil of the lower slope ranged from only 3 to 130 g g^–1. In both the organic mats of the tierra firme and the humic horizon at the lower-slope tall Amazon caatinga site, 50–60% of the P was in inorganic forms, which, in the absence of P-fixing mineral soil, maintain high levels of plant-available P. As a result, the litter mats and humic horizon accounted for over 70% of the total available P in these soils. The proportion of available P increased, and P sorption decreased, downslope, supporting ecological studies which found that tall Amazon caatinga was least P-limited. Soil N and C levels show a maximum at the mid-slope and a minimum at the lower slope. Distributions of biomass C, N and P closely follow those of soil C, N and available (but not total) P along the slope.