Higher-order effects, continuous species interactions, and trait evolution shape microbial spatial dynamics

The assembly and maintenance of microbial diversity in natural communities, despite the abundance of toxin-based antagonistic interactions, presents major challenges for biological understanding. A common framework for investigating such antagonistic interactions involves cyclic dominance games with pairwise interactions. The incorporation of higher-order interactions in such models permits increased levels of microbial diversity, especially in communities in which antibiotic-producing, sensitive, and resistant strains coexist. However, most such models involve a small number of discrete species, assume a notion of pure cyclic dominance, and focus on low mutation rate regimes, none of which well represent the highly interlinked, quickly evolving, and continuous nature of microbial phenotypic space. Here, we present an alternative vision of spatial dynamics for microbial communities based on antagonistic interactions—one in which a large number of species interact in continuous phenotypic space, are capable of rapid mutation, and engage in both direct and higher-order interactions mediated by production of and resistance to antibiotics. Focusing on toxin production, vulnerability, and inhibition among species, we observe highly divergent patterns of diversity and spatial community dynamics. We find that species interaction constraints (rather than mobility) best predict spatiotemporal disturbance regimes, whereas community formation time, mobility, and mutation size best explain patterns of diversity. We also report an intriguing relationship among community formation time, spatial disturbance regimes, and diversity dynamics. This relationship, which suggests that both higher-order interactions and rapid evolution are critical for the origin and maintenance of microbial diversity, has broad-ranging links to the maintenance of diversity in other systems.

Idea paper: An envelope model of ecological disturbance

Disturbance is common in natural ecosystems, but increasingly defines them. While there are many descriptions for the dynamics of an ecosystem's response to disturbance, there are few descriptions for the dynamics of the disturbance itself. I describe a novel application of a model based on the production of amplitude envelopes in acoustics and electronic music synthesis, with varying parameters Attack, Decay, Sustain, and Release (ADSR). I show that varying the parameters of the ADSR model is sufficient to produce and vary the qualitative disturbance regimes described by previous authors, and is capable of producing dynamics not previously considered. I tested the utility of the ADSR model by applying it to a logistic growth model. I found that manipulating the attack and release parameters of the ADSR model changes the population dynamics estimated by these models. This implies that responses to disturbance are determined not only by the resilience and resistance of the ecological system, but also the dynamics of the disturbance itself. My hope is that the ADSR model will prove useful to researchers in either describing disturbances in long-term ecological data, or in producing disturbances for simulations or experiments.

Comparison of Culturing and Metabarcoding Methods to Describe the Fungal Endophytic Assemblage of Brachypodium rupestre Growing in a Range of Anthropized Disturbance Regimes

Fungal endophytes develop inside plants without visible external signs, and they may confer adaptive advantages to their hosts. Culturing methods have been traditionally used to recognize the fungal endophytic assemblage, but novel metabarcoding techniques are being increasingly applied. This study aims to characterize the fungal endophytic assemblage in shoots, rhizomes and roots of the tall grass Brachypodium rupestre growing in a large area of natural grasslands with a continuum of anthropized disturbance regimes. Seven out of 88 taxa identified via metabarcoding accounted for 81.2% of the reads (Helotiaceae, Lachnum sp. A, Albotricha sp. A, Helotiales A, Agaricales A, Mycena sp. and Mollisiaceae C), revealing a small group of abundant endophytes and a large group of rare species. Although both methods detected the same trends in richness and fungal diversity among the tissues (root > rhizome > shoot) and grasslands (low-diversity > high-diversity grasslands), the metabarcoding tool identified 5.8 times more taxa than the traditional culturing method (15 taxa) but, surprisingly, failed to sequence the most isolated endophyte on plates, Omnidemptus graminis. Since both methods are still subject to important constraints, both are required to obtain a complete characterization of the fungal endophytic assemblage of the plant species.

Technical Report: Monitoring and Communicating Changes in Disturbance Regimes (Version 1.0)

Shifts in disturbance patterns across the Northeast are of increasing concern as the climate continues to change. In particular, changes in patterns of frequency, severity and extent of disturbance event may have detrimental cascading impacts on forest ecosystems and human communities. To explore how changing disturbance regimes might impact future forest health and management it is necessary to understand the historical trends and impacts of disturbance in the region. Although individual types of disturbance have already been analyzed, there is a need for a consolidated overview of the current state of disturbance in northeastern forests. To address this need, the Forest Ecosystem Monitoring Cooperative (FEMC) developed the FEMC: Tracking Shifts in Disturbance Regimes web portal for users to explore changes over time of key disturbance drivers, identify important disturbance responses, and discover where monitoring is happening for both drivers and responses. In collaboration with our advisory committee, we identified key disturbance drivers—flood, high winds, fire, drought, pests—and responses—macroinvertebrates, cold-water fisheries, invasive plants—that are of particular concern in the region. For each of the drivers we identified a suitable regional dataset and analyzed changes over time in frequency, severity, and extent. We also created a structured framework to catalogue programs across the region that are monitoring for these disturbance drivers and responses. Version 1.0 of the FEMC: Tracking Shifts in Disturbance Regimes (https://uvm.edu/femc/disturbance) web portal, first released in October 2021, contains 272 data programs, 11 drivers and three responses. Through the web portal users can browse programs by state, driver type or response type, and explore where monitoring is happening across the region. Driver-specific analyses allow users to quickly see the trends in severity, frequency and extent of selected disturbances and compare the impacts in selected states to regional data. We hope that this collection of programs and the analysis of trends provide researchers and land managers with an easy way to understand the current state of disturbance in northeastern forests that enables them to analyze and plan for future impacts.

Persistent impacts of the 2018 drought on forest disturbance regimes in Europe

Europe was affected by an extreme drought in 2018, compounding with an extensive heat wave in the same and subsequent years. Here we provide a first assessment of the impacts this compounding event had on forest disturbance regimes in Europe. We find that the 2018 drought caused unprecedented levels of forest disturbance across large parts of Europe, persisting up to 2 years post-drought. The 2018 drought pushed forest disturbance regimes in Europe to the edge of their past range of variation, especially in central and eastern Europe. Increased levels of forest disturbance were associated with low soil water availability in 2018 and were further modulated by high vapor pressure deficit from 2018 to 2020. We also document the emergence of novel spatiotemporal disturbance patterns following the 2018 drought (i.e., more and larger disturbances, occurring with higher spatiotemporal autocorrelation) that will have long-lasting impacts on forest structure and raise concerns about a potential loss of forest resilience. We conclude that the 2018 drought had unprecedented impacts on forest disturbance regimes in Europe, highlighting the urgent need to adapt Europe's forests to a hotter and drier future with more disturbance.

Natural disturbance regimes for implementation of ecological forestry: a review and case study from Nova Scotia, Canada

Ecological forestry is based on the idea that forest patterns and processes are more likely to persist if harvest strategies produce stand structures, return intervals, and severities similar to those from natural disturbances. Taylor et al. (2020) reviewed forest natural disturbance regimes in Nova Scotia, Canada, to support implementation of ecological forestry. In this follow-up paper, we 1) review use of natural disturbance regimes to determine target harvest rotations, age structures, and residual stand structures; and 2) describe a novel approach for use of natural disturbance regimes in ecological forestry developed for Nova Scotia. Most examples of ecological forestry consider only the local, dominant disturbance agent, such as fire in boreal regions. Our approach included: 1) using current ecological land classification to map potential natural vegetation (PNV) community types; 2) determining cumulative natural disturbance effects of all major disturbances, in our case fire, hurricanes, windstorm, and insect outbreaks for each PNV; and 3) using natural disturbance regime parameters to derive guidelines for ecological forestry for each PNV. We analyzed disturbance occurrence and return intervals based on low, moderate, and high severity classes (<30, 30-60, and >60% of biomass of living trees killed), which were used to determine mean annual disturbance rates by severity class. Return intervals were used to infer target stand age-class distributions for high, moderate, and low severity disturbances for each PNV. The range of variation in rates of high severity disturbances among PNVs was from 0.28% yr-1 in Tolerant Hardwood to 2.1% yr-1 in the Highland Fir PNV, equating to return intervals of 357 years in Tolerant Hardwood to 48 yrs in Highland Fir PNVs. As an example, this return interval for the Tolerant Hardwood PNV resulted in target rotation lengths of 200 years for 35% of the PNV area, 500 years for 40%, and 1000 years for 25%. The proposed approach of determining natural disturbance regimes for PNV communities and calculating target disturbance rates and corresponding harvest rotation lengths or entry times appears to be a feasible method to guide ecological forestry in any region with a strong ecological land classification system and multiple disturbance agents.

Mapping the probability of forest snow disturbances in Finland

The changing forest disturbance regimes emphasize the need for improved damage risk information. Here, our aim was to (1) improve the current understanding of snow damage risks by assessing the importance of abiotic factors, particularly the modelled snow load on trees, versus forest properties in predicting the probability of snow damage, (2) produce a snow damage probability map for Finland. We also compared the results for winters with typical snow load conditions and a winter with exceptionally heavy snow loads. To do this, we used damage observations from the Finnish national forest inventory (NFI) to create a statistical snow damage occurrence model, spatial data layers from different sources to use the model to predict the damage probability for the whole country in 16 x 16 m resolution. Snow damage reports from forest owners were used for testing the final map. Our results showed that best results were obtained when both abiotic and forest variables were included in the model. However, in the case of the high snow load winter, the model with only abiotic predictors performed nearly as well as the full model and the ability of the models to identify the snow damaged stands was higher than in other years. The results showed patterns of forest adaptation to high snow loads, as spruce stands in the north were less susceptible to damage than in southern areas and long-term snow load reduced the damage probability. The model and the derived wall-to-wall map were able to discriminate damage from no-damage cases on a good level (AUC > 0.7). The damage probability mapping approach identifies the drivers of snow disturbances across forest landscapes and can be used to spatially estimate the current and future disturbance probabilities in forests, informing practical forestry and decision-making and supporting the adaptation to the changing disturbance regimes.

The Beautiful and the Dammed: Defining Multi-Stressor Disturbance Regimes in an Atlantic River Floodplain Wetland

Natural hydrological fluctuations within river floodplains generate habitat diversity through variable connections between habitat patches and the main river channel. Human modification of floodplains can alter the magnitude and frequency of large floods and associated sediment movement by interrupting these floodplain connections. The lower Wolastoq | Saint John River and its associated floodplain wetlands are experiencing anthropogenic disturbances arising from climate change, increased urbanization in the watershed, changing upstream agricultural landscape practices, and, most notably, major road and dam construction. By comparing digitized aerial images, we identified key periods of change in wetland extent throughout an ecologically significant component of the floodplain, the Grand Lake Meadows and Portobello Creek wetland complex, with significant erosion evident in coves and backwater areas across the landscape following dam construction and significant accretion around the Jemseg River following highway construction. Connectivity and hydrological regime also influenced other habitat components, namely nutrients and metals retention, as well as the composition of the local macrophyte community. These findings address two key aspects of floodplain management: (1) understanding how hydrological alteration has historically influenced floodplain wetlands can inform us of how the ecosystem may respond under future conditions, such as climate change, and (2) the mechanisms by which habitat diversity and disturbance regimes filter biological communities, with the potential for patches to host a rich biodiversity continuously supporting critical ecosystem functions.

Distribution of Woody Plant Species Among Different Disturbance Regimes of Forests in a Temperate Deciduous Broad-Leaved Forest

Forests in different disturbance regimes provide diverse microhabitats for species growth. However, whether the species distribution of wood plant is random or follows ecological specialization among forests in different disturbance regimes remains to be elucidated. In this study, four 1 hm2 (100 m × 100 m) forest dynamic monitoring plots in different disturbance regimes of forests were randomly selected in a temperate deciduous broad-leaved forest. We examined the specificity of woody plants to forests through network analysis. Torus-translation test was used to analyze the species distribution preference of woody plants to forests in different disturbance regimes. The specialization index of woody plants was 0.3126, and that of shrubs (51.01%) was higher than that of trees (25.16%). Moreover, 66.67% (38/57) of woody plants were associated with different forests. More shrub species (70.00%) had specific preferences than tree species (45.95%) with respect to forests in different disturbance regimes. Our findings suggest that the distribution of woody plants among forests with different disturbance regimes is not random but is specialized. Different woody plants show different community preferences in different disturbance regimes of forests. Shrubs show higher specialization than trees in different disturbance regimes of forests.