Ecological memory preserves phage resistance mechanisms in bacteria

Bacterial defenses against phage, which include CRISPR-mediated immunity and other mechanisms, can carry substantial growth rate costs and can be rapidly lost when pathogens are eliminated. How bacteria preserve their molecular defenses despite their costs, in the face of variable pathogen levels and inter-strain competition, remains a major unsolved problem in evolutionary biology. Here, we present a multilevel model that incorporates biophysics of molecular binding, host-pathogen population dynamics, and ecological dynamics across a large number of independent territories. Using techniques of game theory and non-linear dynamical systems, we show that by maintaining a non-zero failure rate of defenses, hosts sustain sufficient levels of pathogen within an ecology to select against loss of the defense. This resistance switching strategy is evolutionarily stable, and provides a powerful evolutionary mechanism that maintains host-pathogen interactions, selects against cheater strains that avoid the costs of immunity, and enables co-evolutionary dynamics in a wide range of systems.

The emergent past: past natural and human disturbances of trees can reduce their present resistance to drought stress

Forest tree growth is primarily explained, modelled, and predicted depending on current age or size, environmental conditions, and competitive status in the stand. The accumulated size is commonly used as a proxy for a tree's past development. However, recent studies suggest that antecedent conditions may impact present growth by epigenetic, transcriptional, proteomic, or metabolic changes alongside physiological and structural properties. Here, I analysed the ecological memory effect embedded in the xylem as a tree-ring structure. I used 35 mature Norway spruces (Picea abies (L.) H. Karst.) and 36 European beeches (Fagus sylvatica L.) of the Kranzberg Forest water retention experiment KROOF in South Germany to scrutinise how their past development determines the growth of control plots and plots with 5-year water retention. I hypothesised that the current size and growing conditions determine tree growth and drought stress resistance. Metrics quantifying the trees’ recent and past growth, and correlation and linear mixed models with random effects revealed the following ecological memory effects. (1) For both species, the progressive growth course, low inter-annual growth variation in the long term, and low growth deflections in the recent past increased the growth resistance to drought. (2) The correlation between the past growth metrics and current stress reactions revealed that legacy effects could reach back 5–30 years; I found short- and long-term ecological memory. (3) Parameters of model prediction of the basic model with only size as a predictor of tree growth could be improved. The results suggest differences in the internal stem structure and ring pattern cause-specific differences in the trees' functioning and growth. I conclude that a long-term progressive increase and low variation in ring width may improve water conduction and reduce embolism in both species. Annual growth variation and low growth events in the recent past may have primed the morphology and allocation of the Norway spruce to better resist drought. The strong reduction in current growth, drought resistance by irregular growth, and past growth disturbances reveal a memory effect embedded in the tree ring pattern, suggesting further exploration and consideration in tree monitoring, growth modelling, and silvicultural prescriptions.

Ecological memory of recurrent drought modifies soil processes via changes in soil microbial community

Climate change is altering the frequency and severity of drought events. Recent evidence indicates that drought may produce legacy effects on soil microbial communities. However, it is unclear whether precedent drought events lead to ecological memory formation, i.e., the capacity of past events to influence current ecosystem response trajectories. Here, we utilize a long-term field experiment in a mountain grassland in central Austria with an experimental layout comparing 10 years of recurrent drought events to a single drought event and ambient conditions. We show that recurrent droughts increase the dissimilarity of microbial communities compared to control and single drought events, and enhance soil multifunctionality during drought (calculated via measurements of potential enzymatic activities, soil nutrients, microbial biomass stoichiometry and belowground net primary productivity). Our results indicate that soil microbial community composition changes in concert with its functioning, with consequences for soil processes. The formation of ecological memory in soil under recurrent drought may enhance the resilience of ecosystem functioning against future drought events.

Quantifying the impact of ecological memory on the dynamics of interacting communities

Ecological memory refers to the influence of past events on the response of an ecosystem to exogenous or endogenous changes. Memory has been widely recognized as a key contributor to the dynamics of ecosystems and other complex systems, yet quantitative community models often ignore memory and its implications. Recent studies have shown how interactions between community members can lead to the emergence of resilience and multistability under environmental perturbations. We demonstrate how memory can complement such models. We use the framework of fractional calculus to study how the outcomes of a well-characterized interaction model are affected by gradual increases in ecological memory under varying initial conditions, perturbations, and stochasticity. Our results highlight the implications of memory on several key aspects of community dynamics. In general, memory slows down the overall dynamics and recovery times after perturbation, thus reducing the system's resilience. However, it simultaneously mitigates hysteresis and enhances the system's capacity to resist state shifts. Memory promotes long transient dynamics, such as long-standing oscillations and delayed regime shifts, and contributes to the emergence and persistence of alternative stable states. Collectively, these results highlight the fundamental role of memory on ecological communities and provide new quantitative tools to analyse its impact under varying conditions.

Vegetation memory effects and their association with vegetation resilience in global drylands

Vegetation memory describes the effect of antecedent environmental and ecological conditions on the present ecosystem state and has been proposed as an important proxy for vegetation resilience. In particular, strong vegetation-memory effects have been identified in dryland regions, but the factors underlying the spatial patterns of vegetation memory remain unknown. We aim to map the components and drivers of vegetation memory in dryland regions using state-of-the-art climate reanalysis data and refined approaches to identify vegetation-memory characteristics across dryland regions worldwide. Using a framework which distinguishes between intrinsic and extrinsic ecological memory, we show that: (i) intrinsic memory is a much stronger component than extrinsic memory in the majority of dryland regions; and (ii) climate reanalysis data sets change the detection of extrinsic vegetation memory effects in some global dryland regions. Synthesis: Our study offers a global picture of the vegetation response to two climate forcing variables using satellite data, information which is potentially relevant for mapping components and properties of vegetation responses worldwide. However, the large differences in the spatial patterns in intrinsic vegetation memory in our study compared to previous analyses show the overall sensitivity of this component in particular to the initial choice of extrinsic forcing variables. As a result, we caution against using the oversimplified link between intrinsic vegetation-memory and vegetation recovery rates at large spatial scales.

Disentangling the Legacies of Climate and Management on Tree Growth

Legacies of past climate conditions and historical management govern forest productivity and tree growth. Understanding how these processes interact and the timescales over which they influence tree growth is critical to assess forest vulnerability to climate change. Yet, few studies address this issue, likely because integrated long-term records of both growth and forest management are uncommon. We applied the stochastic antecedent modelling (SAM) framework to annual tree-ring widths from mixed forests to recover the ecological memory of tree growth. We quantified the effects of antecedent temperature and precipitation up to 4 years preceding the year of ring formation and integrated management effects with records of harvesting intensity from historical forest management archives. The SAM approach uncovered important time periods most influential to growth, typically the warmer and drier months or seasons, but variation among species and sites emerged. Silver fir responded primarily to past climate conditions (25–50 months prior to the year of ring formation), while European beech and Scots pine responded mostly to climate conditions during the year of ring formation and the previous year, although these responses varied among sites. Past management and climate interacted in such a way that harvesting promoted growth in young silver fir under wet and warm conditions and in old European beech under drier and cooler conditions. Our study shows that the ecological memory associated with climate legacies and historical forest management is species-specific and context-dependent, suggesting that both aspects are needed to properly evaluate forest functioning under climate change.

Ecological memory of prior nutrient exposure in the human gut microbiome

Many ecosystems retain an ecological memory of past conditions that affects responses to future stimuli. However, it remains unknown what mechanisms and dynamics may govern such a memory in microbial communities. Here, in both a human dietary intervention cohort and an artificial gut, we show that the human gut microbiome encodes a memory of past carbohydrate exposures. Changes in the relative abundance of primary degraders were sufficient to enhance metabolism, and these changes were mediated by transcriptional changes within hours of initial exposure. We further found that ecological memory of one carbohydrate species impacted metabolism of others. These findings demonstrate that the human gut microbiome's metabolic potential reflects dietary exposures over preceding days and changes within hours of exposure to a novel nutrient.