Jean P. Gibert’s research while affiliated with Duke University and other places

Understanding how global warming shapes species evolution within communities is a pressing goal of ecology. Temperature affects interacting species and can lead to changes in species interactions, but how that will alter species evolutionary trajectories within complex food webs is poorly understood. Here we address 1) whether different predators affect prey evolution differentially, 2) whether the food web context in which this happens influences prey evolution, 3) whether temperature affects prey evolution directly, and 4) whether ecological interactions mediate how temperature affects prey evolution. We use a combination of mathematical modeling and experimental evolution assays in microbial food webs composed of prey algae and their protists predators. We found that temperature alone doesn't drive prey evolution unless predators are involved. Importantly, the influence of temperature through predation is contingent on the food web structure. This leads to distinct evolutionary trajectories when prey evolves with predators alone or with a competing predator present. Our findings indicate that the species evolution to warming is likely contingent on their specific ecological contexts, suggesting that similar species across different food webs could exhibit diverse evolutionary responses to new climates.

Ecosystem restoration can increase the health and resilience of nature and humanity. As a result, the international community is championing habitat restoration as a primary solution to address the dual climate and biodiversity crises. Yet most ecosystem restoration efforts to date have underperformed, failed, or been burdened by high costs that prevent upscaling. To become a primary, scalable conservation strategy, restoration efficiency and success must increase dramatically. Here, we outline how integrating ten foundational ecological theories that have not previously received much attention — from hierarchical facilitation to macroecology — into ecosystem restoration planning and management can markedly enhance restoration success. We propose a simple, systematic approach to determining which theories best align with restoration goals and are most likely to bolster their success. Armed with a century of advances in ecological theory, restoration practitioners will be better positioned to more cost-efficiently and effectively rebuild the world’s ecosystems and support the resilience of our natural resources.

Microbial respiration alone releases massive amounts of Carbon (C) into the atmosphere per year, greatly impacting the global C cycle that fuels climate change. Larger microbial population growth often leads to larger standing biomass, which in turns leads to higher respiration. How rising temperatures might influence microbial population growth, however, depends on how microbial thermal performance curves (TPCs) governing this growth may adapt in novel environments. This thermal adaptation will in turn depend on there being heritable genetic variation in TPCs for selection to act upon. While intraspecific variation in TPCs is traditionally viewed as being mostly environmental (E, or plastic) as a single individual can have an entire TPC, our study uncovers substantial heritable genetic variation (G) and Gene-by-Environment interactions (GxE) in the TPC of a widely distributed ciliate microbe. G results in predictable evolutionary responses to temperature-dependent selection that ultimately shape TPC adaptation in a warming world. Through mathematical modeling and experimental evolution assays we also show that TPC GxE leads to predictable temperature-dependent shifts in population genetic makeup that constrains the potential for future adaptation to warming. That is, adaptive evolution can select for decreased genetic variation which subsequently lowers the evolutionary potential of microbial TPCs. Our study reveals how temperature-dependent adaptive evolution shapes microbial population growth, a linchpin of global ecosystem function, amidst accelerating climate warming.

Temperature significantly impacts microbial communities’ composition and function, which subsequently plays a vital role in the global carbon cycle that ultimately fuels climate change. Interactions between different microorganisms might be critical in shaping how these communities react to both temperature changes. Additionally, rising temperatures are occurring in the context of increasingly nutrient-rich ecosystems due to human activity. Nonetheless, we lack a comprehensive understanding of how predation influences microbial communities in future climate scenarios and an increasingly nutrient-rich world. Here, we assess whether predation by key bacterial consumers—ciliates—influences a microbial community’s freshwater temperature and nutrient response regarding biomass, diversity, structure, and function. In a three-week microcosm experiment, we exposed mostly prokaryotic microbial communities to a community of ciliate predators at two different temperature scenarios (ambient and +3°C, i.e., a conservative projection of climate change by 2050) and nutrient levels (low and elevated). Nutrients, temperature, and ciliate presence influenced microbial biomass and function separately, but their interaction had the largest explanatory power over the observed changes in microbial community biomass, structure, and function. Our study supports previous findings that temperature and nutrients are essential drivers of microbial community structure and function but also demonstrates that the presence of predators can mediate these effects, indicating that the biotic context is as important as the abiotic context to understand microbial responses to novel climates. Importance While the importance of the abiotic environment in microbial communities has long been studied, how prevalent ecological interactions, like predation and the broader abiotic context, may influence these responses is largely unknown. Our study disentangles the complex interplay between temperature, nutrients, and predation and their joint effects on microbial community diversity and function. The findings suggest that while temperature and nutrients are fundamental drivers of microbial community dynamics, the presence of predators significantly mediates these responses. Our study underscores the profound impact of abiotic factors on microbial communities, but how to properly understand, let alone predict, these responses, we need to account for the biotic context in which these are occurring.

Microbes affect the global carbon cycle that influences climate change and are in turn influenced by environmental change. Here, we use data from a long‐term whole‐ecosystem warming experiment at a boreal peatland to answer how temperature and CO 2 jointly influence communities of abundant, diverse, yet poorly understood, non‐fungi microbial Eukaryotes (protists). These microbes influence ecosystem function directly through photosynthesis and respiration, and indirectly, through predation on decomposers (bacteria and fungi). Using a combination of high‐throughput fluid imaging and 18S amplicon sequencing, we report large climate‐induced, community‐wide shifts in the community functional composition of these microbes (size, shape, and metabolism) that could alter overall function in peatlands. Importantly, we demonstrate a taxonomic convergence but a functional divergence in response to warming and elevated CO 2 with most environmental responses being contingent on organismal size: warming effects on functional composition are reversed by elevated CO 2 and amplified in larger microbes but not smaller ones. These findings show how the interactive effects of warming and rising CO 2 levels could alter the structure and function of peatland microbial food webs—a fragile ecosystem that stores upwards of 25% of all terrestrial carbon and is increasingly threatened by human exploitation.

Predators have a key role in structuring ecosystems1–4. However, predator loss is accelerating globally4–6, and predator mass-mortality events⁷ (MMEs)—rapid large-scale die-offs—are now emblematic of the Anthropocene epoch⁶. Owing to their rare and unpredictable nature⁷, we lack an understanding of how MMEs immediately impact ecosystems. Past predator-removal studies2,3 may be insufficient to understand the ecological consequences of MMEs because, in nature, dead predators decompose in situ and generate a resource pulse⁸, which could alter ensuing ecosystem dynamics by temporarily enhancing productivity. Here we experimentally induce MMEs in tritrophic, freshwater lake food webs and report ecological dynamics that are distinct from predator losses2,3 or resource pulses⁹ alone, but that can be predicted from theory⁸. MMEs led to the proliferation of diverse consumer and producer communities resulting from weakened top-down predator control1–3 and stronger bottom-up effects through predator decomposition⁸. In contrast to predator removals alone, enhanced primary production after MMEs dampened the consumer community response. As a consequence, MMEs generated biomass dynamics that were most similar to those of undisturbed systems, indicating that they may be cryptic disturbances in nature. These biomass dynamics led to trophic decoupling, whereby the indirect beneficial effects of predators on primary producers are lost and later materialize as direct bottom-up effects that stimulate primary production amid intensified herbivory. These results reveal ecological signatures of MMEs and demonstrate the feasibility of forecasting novel ecological dynamics arising with intensifying global change.

Mixotrophs are ubiquitous and integral to microbial food webs, but their impacts on the dynamics and functioning of broader ecosystems are largely unresolved. Here, we show that mixotrophy produces a unique type of food web module that exhibits unusual ecological dynamics, with surprising consequences for carbon flux under warming. We develop a generalizable model of a mixotrophic food web module that incorporates dynamic switching between phototrophy and phagotrophy to assess ecological dynamics and total system CO2 flux. We find that warming switches mixotrophic systems between alternative stable carbon states—including a phototrophy‐dominant carbon sink state, a phagotrophy‐dominant carbon source state and cycling between these two. Moreover, warming always shifts this mixotrophic system from a carbon sink state to a carbon source state, but a coordinated increase in nutrients can erase early warning signals of this transition and expand hysteresis. This suggests that mixotrophs can generate critical carbon tipping points under warming that will be more abrupt and less reversible when combined with increased nutrient levels, having widespread implications for ecosystem functioning in the face of rapid global change. Read the free Plain Language Summary for this article on the Journal blog.

Microbes play a major role in the global carbon cycle that fuels climate change. But how microbes may in turn respond to climate change remains poorly understood. Here, we collect data from a long-term whole-ecosystem warming experiment at a boreal peatland to address how temperature and carbon dioxide jointly influence protist communities: i.e., abundant and diverse, but poorly understood, microbial Eukaryotes. Protists influence ecosystem function directly through photosynthesis and respiration, and indirectly through predation on decomposers (bacteria, archaea, and fungi). Using a combination of high-throughput fluid imaging and 18S amplicon sequencing, we report climate-induced, community-wide shifts in protist community functional composition (e.g., size, shape, and metabolism) that could alter the overall function of peatland ecosystems. We also show that these responses to warming and elevated carbon dioxide are the result of taxonomic turnover. Surprisingly, our results clearly show strong interactive effects between temperature and carbon dioxide, such that the effects of warming on functional composition are generally reversed by elevated carbon dioxide. These findings show how the interactive effects of warming and rising carbon dioxide could alter the structure and function of peatland microbial food webs: a fragile ecosystem that stores 25% of terrestrial carbon and is increasingly threatened by human exploitation.

Climate change is affecting how energy and matter flow through ecosystems, thereby altering global carbon and nutrient cycles. Microorganisms play a fundamental role in carbon and nutrient cycling and are thus an integral link between ecosystems and climate. Here, we highlight a major black box hindering our ability to anticipate ecosystem climate responses: viral infections within complex microbial food webs. We show how understanding and predicting ecosystem responses to warming could be challenging—if not impossible—without accounting for the direct and indirect effects of viral infections on different microbes (bacteria, archaea, fungi, protists) that together perform diverse ecosystem functions. Importantly, understanding how rising temperatures associated with climate change influence viruses and virus-host dynamics is crucial to this task, yet is severely understudied. In this perspective, we 1) synthesize existing knowledge about virus-microbe-temperature interactions and 2) identify important gaps to guide future investigations regarding how climate change might alter microbial food web effects on ecosystem functioning. To provide real-world context, we consider how these processes may operate in peatlands—globally significant carbon sinks that are threatened by climate change. We stress that understanding how warming affects biogeochemical cycles in any ecosystem hinges on disentangling complex interactions and temperature responses within microbial food webs.

Anthropogenic increases in temperature and nutrient loads will likely impact food web structure and stability. Although their independent effects have been reasonably well studied, their joint effects-particularly on coupled ecological and phenotypic dynamics-remain poorly understood. Here we experimentally manipulated temperature and nutrient levels in microbial food webs and used time-series analysis to quantify the strength of reciprocal effects between ecological and phenotypic dynamics across trophic levels. We found that (1) joint-often interactive-effects of temperature and nutrients on ecological dynamics are more common at higher trophic levels, (2) temperature and nutrients interact to shift the relative strength of top-down versus bottom-up control, and (3) rapid phenotypic change mediates observed ecological responses to changes in temperature and nutrients. Our results uncover how feedback between ecological and phenotypic dynamics mediate food web responses to environmental change. This suggests important but previously unknown ways that temperature and nutrients might jointly control the rapid eco-phenotypic feedback that determine food web dynamics in a changing world.