Anthropogenic disturbance equalizes diversity levels in arbuscular mycorrhizal fungal communities

The arbuscular mycorrhizal (AM) symbiosis is a key plant–microbe interaction in sustainable functioning ecosystems. Increasing anthropogenic disturbance poses a threat to AM fungal communities worldwide, but there is little empirical evidence about its potential negative consequences. In this global study, we sequenced AM fungal DNA in soil samples collected from pairs of natural (undisturbed) and anthropogenic (disturbed) plots in two ecosystem types (10 naturally wooded and six naturally unwooded ecosystems). We found that ecosystem type had stronger directional effects than anthropogenic disturbance on AM fungal alpha and beta diversity. However, disturbance increased alpha and beta diversity at sites where natural diversity was low and decreased diversity at sites where natural diversity was high. Cultured AM fungal taxa were more prevalent in anthropogenic than natural plots, probably due to their efficient colonization strategies and ability to recover from disturbance. We conclude that anthropogenic disturbance does not have a consistent directional effect on AM fungal diversity; rather, disturbance equalizes levels of diversity at large scales and causes changes in community functional structure.     

Disturbance–diversity models: what do they really predict and how are they tested?

The intermediate disturbance hypothesis (IDH) and the dynamic equilibrium model (DEM) are influential theories in ecology. The IDH predicts large species numbers at intermediate levels of disturbance and the DEM predicts that the effect of disturbance depends on the level of productivity. However, various indices of diversity are considered more commonly than the predicted number of species in tests of the hypotheses. This issue reaches beyond the scientific community as the predictions of the IDH and the DEM are used in the management of national parks and reserves. In order to compare responses with disturbance among measures of biodiversity, we used two different approaches of mathematical modelling and conducted an extensive meta-analysis. Two-thirds of the surveyed studies present different results for different diversity measures. Accordingly, the meta-analysis showed a narrow range of negative quadratic regression components for richness, but not evenness. Also, the two models support the IDH and the DEM, respectively, when biodiversity is measured as species richness, but predict evenness to increase with increasing disturbance, for all levels of productivity. Consequently, studies that use compound indices of diversity should present logical arguments, a priori, to why a specific index of diversity should peak in response to disturbance.     

Causes of species diversity differences: a comparative analysis of Markov models

While many dynamic processes have been proposed to produce diversity differences among communities, most empirical investigations focus on static system attributes. An ideal analysis would consider multiple dynamic processes and their impact on many community members, but such analyses can be logistically daunting. I compared Markov chain models of ecological communities to explore general processes leading to diversity differences of sessile species between coral reefs and rocky intertidal mussel beds. As predicted by diversity theory, high diversity coral reefs had lower species replacement probabilities and higher disturbance rates than did lower diversity mussel beds. Intransitivities in species replacements, recruitment limitation and responses to perturbing species from equilibrium (Jacobian elements) did not differ significantly between systems. Tradeoffs between the displacement risk or displacement ability of a species and either disturbance risk or colonising ability were not apparent. Manipulating the coral reef model to eliminate disturbance or intransitivities caused declines in species diversity, whereas removing recruitment limitation or increasing the probability of interspecific replacement did not. Higher overall disturbance levels can explain part of the diversity difference between systems, but much remained unexplained, indicating that details of the pattern and strengths of species interactions were probably extremely important.     

Hypertrophic phytoplankton and the Intermediate Disturbance Hypothesis

The provisions of Connell's Intermediate Disturbance Hypothesis (IDH) were investigated in relation to the behaviour of freshwater phytoplankton in a hypertrophic lagoon, paying special attention to the link between species-diversity and environmental disturbances. Phytoplankton diversity yielded different indices depending on the basic unit of calculations (cells, particles, phytoplankton units, biomass). Although their ranges were approximately equal, they did not covary so could not be considered mutually substitutable. For the purpose of IDH testing, biomass diversity was chosen.Equilibrium states were considered to obtain in those periods with a very high fraction of total phytoplankton biomass, shared by no more than three phytoplankton species. Disturbances were considered as counterparts of equilibrium states. Disturbance factors were mostly abiotic, environmental features of the lake operating on the phytoplankton community at different time scales (co-occurring and with 1- and 2-weeks' lags). These scales may relate to the time required to establish phytoplankton community structure.IDH could be suspected not to hold for the phytoplankton of this hypertrophic lake, which experienced seven near-equilibrium phases and six disturbance periods throughout the study. As a rule, equilibrium states lasted longer than disturbance periods. The expected relationships between both disturbance intensity or frequency were not shown. Furthermore, no relationship was demonstrated between diversity (and hence IDH) and the phytoplankton community change rate. Wind stress probably played a minor role in triggering disturbance events. Disturbances were shown partly to promote small-sized phytoplankton communities.Finally, a plea for studying hypertrophic phytoplankton in greater detail is stressed if its responses to disturbances are to be fully understood.     

Interactions between frequency and size of disturbance affect competitive outcomes

Disturbance has many effects on ecological communities, and it is often suggested that disturbance can affect species diversity by altering competitive outcomes. However, disturbance regimes have many distinct aspects that may act, and interact, to influence species diversity. While there are many theoretical models of disturbance-prone communities, few have specifically documented how interactions between different aspects of a disturbance regime change competitive outcomes. Here, we present a model of two plant species subject to disturbance which we then use to examine species coexistence over varying levels of two aspects of disturbance: frequency, and spatial extent (i.e., area disturbed). We show that the competitive outcome is affected differently by changes in each aspect and that the effect of disturbance frequency on species coexistence depends strongly on the spatial extent of the disturbance, and vice versa. We classify the nature of these interactions between disturbance frequency and extent on the basis of the shape of the resulting coexistence regions in a frequency?Cextent parameter plane. Our results illustrate that different types of interaction can result from differences in life-history traits that control species-specific sensitivity to frequency and extent of disturbance. Thus, our analysis shows that the various aspects of disturbance must be carefully considered in concert with the life-history traits of the community members in order to assess the consequences of disturbance.     

The dynamics of the diversity–energy relationship during the last 21,000 years

Aim

Spatial diversity patterns are linked to energy availability, but how the diversity–energy relationship changes in space and time is unclear. There are three possible scenarios: (a) equilibrium dynamics, where diversity is always positively related to energy availability in both time and space; (b) out-of-equilibrium dynamics, where diversity is determined by energy availability in equilibrium, but diversity variation lags behind changes in energy availability, leading to a mismatch between temporal and spatial diversity–energy relationships; and (c) disequilibrium dynamics where the equilibrium does not exist or is irrelevant. We attempt to distinguish these scenarios using spatio-temporal palaeoecological data.

Location

USA and Canada.

Time period

21,000–1,000 years before present.

Major taxa studied

Woody plants.

Methods

We tested for the strength and direction of temporal and spatial relationships between pollen type diversity of woody species and energy availability (estimated from temperature and precipitation) in 1,000-year time steps.

Results

Whereas the temporal diversity–energy relationship appears only when energy levels rapidly change, the spatial diversity–energy relationship is pronounced only when these levels stabilize.

Main conclusions

Our findings are consistent with the out-of-equilibrium scenario – diversity equilibria do exist and act as attractors of diversity dynamics, but diversity is often out of equilibrium. Consequently, current rapid climate changes can disrupt spatially consistent diversity–energy relationships. To understand diversity dynamics, it is crucial to simultaneously consider both the spatial and temporal dimensions of diversity variation.     

Assessing the effect of sound file compression and background noise on measures of acoustic signal structure

The study of animal acoustic signals is a central tool for many fields in ecology and evolution, but the diversity of analytical methods and sources of animal sound recordings poses important challenges for carrying out robust acoustic analyses. Sound file compression and background noise may both affect acoustic analysis, although little attention has been paid to their respective effects. We evaluated the effect of these factors by assessing the systematic deviation (i.e. bias) and measurement error (i.e. precision) that they generate on spectrographic parameters and two (dis)similarity methods (dynamic time warping on frequency contours and cross-correlation), which represent the most common methods currently used for quantitative characterization of acoustic signals. Measurements were taken across a wide range of signals from a diverse group of bird species, and compared between uncompressed files and decompressed files obtained from mp3-encoded files generated using the two most common mp3 encoders (Fraunhofer and LAME). Measurements were also compared across a range of synthetically-generated background noise levels. Compression did not significantly bias any of the acoustic or similarity measurements. However, the precision of acoustic parameters representing single extreme values (e.g. peak frequency) as well as dynamic time warping distances, was strongly affected by compression. High background noise biased most energy distribution-related parameters (e.g. spectral entropy) and affected the precision of most acoustic parameters and dynamic time warping. Overall, compression and background noise did have considerable effects on acoustic analyses. We provide recommendations to avoid potential pitfalls and maximize the information that can be reliably obtained.     

Issues affecting the measurement of disturbance response patterns in herbaceous vegetation – A test of the intermediate disturbance hypothesis

The 'intermediate disturbance hypothesis' (IDH) predicts maximum species diversity at intermediate levels of disturbance. Disturbance levels are measured by intensity or frequency of disturbance or by the time since disturbance. The IDH has been tested over a wide range of studies and communities with results either accepting or rejecting the hypothesis. The objectives of this study were to determine how observed disturbance response patterns for the same herbaceous plant community are influenced by modelling techniques, particularly in relation to the expression of disturbance gradients, choice of species diversity indices, and time of assessment since disturbance. Response patterns were examined using a multi-factorial disturbance experiment involving grazing (absent and present); fire (absent and present); soil cultivation (none, 5 and 20 cm); and amendment (none, fertiliser, and fertiliser plus clover seeds). Generalized linear models with a b-spline function were used to define response patterns for five different disturbance gradients over a 24-month period using three indices of diversity. Seven basic disturbance response models were recognized ranging from the classical IDH bell-shaped pattern through increasing or decreasing trends, to a no-change model with increasing levels of disturbance. Only 6.7% of all models were consistent with the IDH. The no-change model was found in nearly half the cases investigated and increased in occurrence with time since disturbance. The choice of the disturbance intensity gradient, the species diversity index used and the time of assessment after disturbance significantly influenced the frequency of occurrence of the disturbance response models observed. Consequently, the responses of vegetation to disturbance gradients show many patterns depending on how they are defined and modelled rather than the simple bell-shaped curve as predicted by the IDH, but the ecological mechanisms supporting some of these patterns need to be further investigated.     

Comparing Neutral and Trade-off Community Models in Shaping the Community Biomass-Diversity Relationship Under Different Disturbance Levels

Among numerous mechanisms shaping the unimodal relationship between diversity and community biomass, the trade-off model of “CRS” theory is the most famous one. However, recent researches indicate that this relationship may also emerge under the neutral model where all species are identical with each other. By using an individual-based spatially-explicit model, we evaluated the underlying mechanisms shaping this curve for both models under different disturbance levels. We found unimodal relationships emerged for both models at low and medium disturbance levels; the richness for the trade-off community was lower than the neutral community for most of the environment severity levels, especially at the benign environment due to the strong competitive exclusions among species. Whereas under high disturbance level, the positive relationships emerged for both models; both communities had similar richness with their curves nearly overlapped with each other, that is, because the high disturbance intensity strongly decreased the competitive exclusions within the trade-off community. Our results indicate that although the underlying mechanisms are totally different, both models will produce the similar relationship between diversity and community biomass under different disturbance levels.     

A long-term experimental test of the dynamic equilibrium model of species diversity

The dynamic equilibrium model of species diversity predicts that ecosystem productivity interacts with disturbance to determine how many species coexist. However, a robust test of this model requires manipulations of productivity and disturbance over a sufficient timescale to allow competitive exclusion, and such long-term experimental tests of this hypothesis are rare. Here we use long-term (27 years), large-scale (8 × 50-m plots), factorial manipulations of soil resource availability and sheep grazing intensity (disturbance) in grasslands to test the dynamic equilibrium model. As predicted by the model, increased productivity not only reduced plant species richness, but also moderated the effects of grazing intensity, shifting them from negative to neutral with increasing productivity. Reductions in species richness with productivity were associated with dominance by faster growing (i.e. high specific leaf area) and taller plants. Conversely, grazing favoured shorter plants and this effect became stronger with greater productivity, consistent with the view that grazing can lead to weaker asymmetric competition for light. Our study shows that the dynamic equilibrium model can help to explain changes in plant species richness following long-term increases in soil resource availability and grazing pressure, two fundamental drivers of change in grasslands worldwide.     

Gap formation and species diversity in Japanese beech forests: a test of the intermediate disturbance hypothesis on a geographic scale

To evaluate whether the intermediate-disturbance hypothesis applies on regional scales, the relationship between the species diversity and gap formation regime of beech forests was examined. The mean gap size and the variation of gap sizes showed no correlation with species diversity. The mean windstorm interval varied widely, but geographical trends, such as latitudinal gradient, were not observed. However, locations that sustained an intermediate frequency of disturbance had the highest species diversity. Although a latitudinal gradient of disturbance was not apparent, the intermediate-disturbance hypothesis was partly supported on a geographic scale. The most predictable model for species diversity was a multiple regression model composed of two factors, the windstorm interval and the cumulative temperature of the growing season. The fact that the temperature was of greater importance than the disturbance interval indicates that the most important factor in predicting forest species diversity is the amount of available energy on a geographic scale.     

Predicting invertebrate diversity from disturbance regimes in forest streams

The link between substrate disturbance and stream invertebrate species richness is often complicated by the fact that substrate disturbance removes both invertebrates and periphyton (a potential food source). It is never clear whether disturbance acts directly on species diversity by removing animals or indirectly by reducing one of their food sources. To examine this relationship invertebrate diversity patterns were examined in 25 forest streams in Urewera National Park, New Zealand, where light attenuation from the forest canopy was postulated to limit periphyton biomass and remove the confounding influence of periphyton on the link between substrate disturbance and invertebrate diversity. Invertebrate species richness declined linearly with increasing substrate disturbance. Although periphyton biomass was comparatively low, species richness was more strongly related to periphyton biomass than to any disturbance measure. The highly mobile nature and terrestrial reproductive stage of many lotic invertebrates suggest that colonisation dynamics may have a more important influence on diversity patterns than monopolisation of resources for population growth. Although both the intermediate disturbance hypothesis and the dynamic equilibrium model encompass colonisation as a critical determinant of diversity both models also require a trade-off between the colonising and competitive ability of individual species; a phenomenon which does not appear to occur widely in lotic communities. Rather, it is postulated that resource levels will set an upper limit to the species richness of a benthic community that can be achieved through colonisation of taxa in the absence of disturbance, while disturbance removes taxa and resets the colonisation process.     

Disturbance regimes and vegetation dynamics: role of floods in riverine wetlands

Abstract. This study tested whether the frequency of flood disturbances was able to slow down or stabilize vegetation succession in former braided channels over a decade. According to the Patch Dynamics Concept and to succession theory, species richness and diversity should be high but stable in the frequently (40 days/year) flooded channel, and should change over time in the infrequently (1 day/year) flooded one. Within the frequently disturbed channel, composition of vegetation as well as species richness and diversity appeared stable through dynamic equilibrium over the decade. Only one zone, because of particular geomorphological features that decreased disturbance intensity, developed highest diversity and richness as expected from the Intermediate Disturbance Hypothesis. The highest disturbance effect decreased species richness and was related to a higher spatial heterogeneity of the substrate (number of grain-size classes). In the other zones, richness and diversity appeared to be lowest where disturbance frequency was lowest or disturbance intensity was highest. From 1981 to 1987, the infrequently flooded channel underwent succession, and species richness increased in the major part of the channel, whereas diversity increased only in its extreme parts.     

Effect of Habitat Patch Characteristics on Abundance and Diversity of Insects in an Agricultural Landscape

The objective of this study was to test for general effects of patch size, patch isolation, disturbance frequency, and patch life span, on density and diversity of organisms. We sampled predominantly herbivorous insects in 31 alfalfa fields that varied in size, isolation, frequency of disturbance by cutting, and age (number of years planted in alfalfa). Effects on insect relative density and diversity were examined at three taxonomic levels: all insects, eight separate orders, and six legume-specialist weevil species. We found that (a) more isolated alfalfa fields had higher overall insect richness, (b) fields with higher disturbance frequency had lower overall insect richness, and (c) fields of intermediate age had highest insect richness. In some cases these patterns were reflected at lower taxonomic levels, but in many cases they were not. These results are important because they indicate that, although we cannot simultaneously tailor a landscape for each of thousands of species, we may be able to produce desired effects at a more general level. Received 8 August 1997; accepted 2 January 1998.     

Is high species richness at intermediate disturbance level valuable for phylogenetic conservation? A test on bird species in South‐East Botswana

The intermediate disturbance hypothesis (IDH) is one of the most debated theories in ecology. However, even when evidence is provided to support the hypothesis, its relevance for phylogenetic conservation has rarely been tested. Here, we investigated this question on birds in the South‐East district of Botswana along a disturbance gradient across three types of landscapes. We first reconstructed the phylogeny for all species recorded. Next, we assessed the relationship between dissimilarity measures and habitat types using the permutational MANOVA. Finally, we tested the IDH by fitting a generalized linear mixed effect model to account for errors due to spatial pseudo‐replications of our collection design. We found that, although species richness and phylogenetic diversity (PD) follow the prediction of the IDH, the evolutionary component of PD (i.e. PSV, phylogenetic species variability) contributes little to the prediction, suggesting that the correlation between PD and disturbance level is driven by the richness component of PD (i.e. PSR, phylogenetic species richness). However, the increased richness at the intermediate disturbance level does not result in phylogenetically diverse bird communities, indicating that the IDH contributes little to phylogenetic diversity. Our study adds to the body of literature questioning the relevance of IDH in ecology.     

The effects of vertical mixing on a phytoplankton community: a modelling approach to the intermediate disturbance hypothesis

1.  Connell's (1978) intermediate disturbance hypothesis (IDH) has been proposed as one explanation of why diversity is often highest at intermediate levels of disturbance. We used a model phytoplankton responses to environmental change (PROTECH) to investigate the validity of this hypothesis.
2. In a simulated phytoplankton assemblage of eight species, we found that the relationship between the increased intensity of a single forcing event and diversity was described by a positively skewed curve.
3. A progressive increase in forcing frequency introduced a sharp decrease in diversity at a threshold frequency. However, the highest diversity values were found at an intermediate frequency of disturbance.
4. We described the shape of this breakpoint response as like a 'cliff' and reconcile it with multiple stable-point theory. It is argued that the IDH should possibly be represented by this 'cliff' relationship, which may be applied to (or encourage the re-examination of) many previous studies.     

Linking species diversity to the functioning of ecosystems: on the importance of environmental context

There is currently much interest in understanding how loss of biodiversity might alter ecological processes vital to the functioning of ecosystems. Unfortunately, ecologists have reached little consensus regarding the importance of species diversity to ecosystem functioning because empirical studies have not demonstrated any consistent relationship between the number of species in a system and the rates of ecological processes. We present the results of a simple model that suggests there may be no single, generalizable relationship between species diversity and the productivity of an ecosystem because the relative contributions of species to productivity change with environmental context. The model determined productivity for landscapes varying in species diversity (the number of species in the colonist pool), spatial heterogeneity (the number of habitat types composing the landscape), and disturbance regimes (+/? a non‐selective mortality). Linear regressions were used to relate species diversity and productivity for each of the environmental contexts. Disturbance changed the form of the diversity/productivity relationship by reducing the slope (i.e. the change in productivity per species added to the colonist pool), but spatial heterogeneity increased or decreased this slope depending on the particular habitat types composing the landscape. The cause of the diversity/productivity relationship also changed with environmental context. The amount of variation in productivity explained by species diversity always increased with spatial heterogeneity, while the amount of variation explained by species composition (i.e. the particular species composing the colonist pool) tended to increase with disturbance. These results lead us to conclude that the form and cause of the relationship between species diversity and productivity may be highly dynamic‐changing over both time and space. Because the trends resulted from well‐known mechanisms by which environmental variation alters the absolute and relative abundances of taxa, we suspect this conclusion may be applicable to many different systems.     

Comparison of the response of meio- and macrobenthos to disturbance and organic enrichment

The effects of the interaction between physical disturbance and organic enrichment with respect to various aspects of subtidal meiobenthic nematode community structure have been examined in a large-scale mesocosm experiment. The relationship between meiobenthic and macrobenthic community structure within this experiment has been explored. Meiofauna and macrofauna showed similar and strongly related responses. Highest diversity was observed in treatment combinations of low levels of disturbance and enrichment and this supports the “Dynamic Equilibrium Model” of Huston [Huston, M.A., 1979. A general hypothesis of species diversity. Am. Nat. 113, 81-101.]. Faunal community structure was more variable at treatment combinations of low levels of disturbance and high levels of organic enrichment. Physical disturbance subdued the effects of high levels of nutrient enrichment. The meio-macrobenthic comparison has been extended to other studies where both meiofaunal and macrofaunal responses have been determined. The response of meiobenthos is often, but not always, the same as that of macrobenthos. These inconsistencies can probably be explained by the constraints of the experimental design of the mesocosm, where macrobenthic recruitment is not possible, as well as the different ecology of these two faunal groups.     

Exploring the energy landscape of antibody-antigen complexes: protein dynamics, flexibility, and molecular recognition

The production of antibodies that selectively bind virtually any foreign compound is the hallmark of the immune system. While much is understood about how sequence diversity contributes to this remarkable feat of molecular recognition, little is known about how sequence diversity impacts antibody dynamics, which is also expected to contribute to molecular recognition. Toward this goal, we examined a panel of antibodies elicited to the chromophoric antigen fluorescein. On the basis of isothermal titration calorimetry, we selected six antibodies that bind fluorescein with diverse binding entropies, suggestive of varying contributions of dynamics to molecular recognition. Sequencing revealed that two pairs of antibodies employ homologous heavy chains that were derived from common germline genes, while the other two heavy chains and all six of the light chains were derived from different germline genes and are not homologous. Interestingly, more than half of all the somatic mutations acquired during affinity maturation among the six antibodies are located in positions unlikely to contact fluorescein directly. To quantify and compare the dynamics of the antibody-fluorescein complexes, three-pulse photon echo peak shift and transient grating spectroscopy were employed. All of the antibodies exhibited motions on three distinct time scales, ultrafast motions on the <100 fs time scale, diffusive motions on the picosecond time scale, and motions that occur on time scales longer than nanoseconds and thus appear static. However, the exact frequency of the picosecond time scale motion and the relative contribution of the different motions vary significantly among the antibody-chromophore complexes, revealing a high level of dynamic diversity. Using a hierarchical model, we relate the data to features of the antibodies' energy landscapes as well as their flexibility in terms of elasticity and plasticity. In all, the data provide a consistent picture of antibody flexibility, which interestingly appears to be correlated with binding entropy as well as with germline gene use and the mutations introduced during affinity maturation. The data also provide a gauge of the dynamic diversity of the antibody repertoire and suggest that this diversity might contribute to molecular recognition by facilitating the recognition of the broadest range of foreign molecules.     

The intermediate disturbance hypothesis does not explain fire and diversity pattern in fynbos

The intermediate disturbance hypothesis is a widely accepted generalization regarding patterns of species diversity, but may not hold true where fire is the disturbance. In the Mediterranean-climate shrublands of South Africa, called fynbos, fire is the most importance disturbance and a controlling factor in community dynamics. The intermediate disturbance hypothesis states that diversity will be highest at sites that have had an intermediate frequency of disturbance and will be lower at sites that have experienced very high or very low disturbance frequencies. Measures of diversity are sensitive to scale; therefore, we compared species richness for three fire regimes in South African mountain fynbos to test the intermediate disturbance hypothesis over different spatial scales from 1 m² to 0.1 hectares. Species diversity response to fire frequency was highly scale-dependent, but the relationship between species diversity and disturbance frequency was opposite that predicted by the intermediate disturbance hypothesis. At the largest spatial scales, species diversity was highest at the least frequently burned sites (40 years between fires) and lowest at the sites of moderate (15 to 26 years between fires) and high fire frequency (alternating four and six year fire cycle). Community heterogeneity, measured both as the slope of the species-area curve for a site and as the mean dissimilarity in species composition among subplots within a site, correlated with species diversity at the largest spatial scales. Community heterogeneity was highest at the least frequently burned sites and lowest at the sites that experienced an intermediate fire frequency.