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1. Exploring Microbiome Functional Dynamics through Space and Time with Trait-Based Theory

   https://doi.org/10.1128/mSystems.00530-21  

   Bittleston, Leonora S.; Freedman, Zachary B.; Bernardin, Jessica R.; Grothjan, Jacob J.; Young, Erica B.; Record, Sydne; Baiser, Benjamin; Gray, Sarah M.; Malik, Ashish (August 2021, mSystems)

   Shade, Ashley (Ed.)

   ABSTRACT Microbiomes play essential roles in the health and function of animal and plant hosts and drive nutrient cycling across ecosystems. Integrating novel trait-based approaches with ecological theory can facilitate the prediction of microbial functional traits important for ecosystem functioning and health. In particular, the yield-acquisition-stress (Y-A-S) framework considers dominant microbial life history strategies across gradients of resource availability and stress. However, microbiomes are dynamic, and spatial and temporal shifts in taxonomic and trait composition can affect ecosystem functions. We posit that extending the Y-A-S framework to microbiomes during succession and across biogeographic gradients can lead to generalizable rules for how microbiomes and their functions respond to resources and stress across space, time, and diverse ecosystems. We demonstrate the potential of this framework by applying it to the microbiomes hosted by the carnivorous pitcher plant Sarracenia purpurea , which have clear successional trajectories and are distributed across a broad climatic gradient. 

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2. A framework for utilizing leaf-associated microbes to achieve conservation and restoration goals

   https://doi.org/10.1128/msphere.01082-24  

   Heil, Jacob A; Bernardin, Jessica R; Galla, Stephanie J; Bittleston, Leonora S (June 2025, mSphere)

   Tringe, Susannah Green (Ed.)

   ABSTRACT Plant-associated microbiomes have profound effects on ecosystem functioning and play a role in the success of plants at both small and large scales. As key components of healthy plants and ecosystems, plant microbiomes should be considered in conservation and ecosystem management strategies. Many knowledge gaps and logistical barriers exist that increase the difficulty of employing microbes in conservation; however, some success has been achieved by manipulating the root microbiome and in agricultural contexts. In contrast with the root microbiome, the role of the leaf microbiome in conservation remains largely unexplored. In this perspective, we posit that the leaf microbiome plays an essential role in plant and ecosystem health and should be considered in conservation strategies. We include a framework for approaching leaf microbiome management, including identification of sources of disturbance, identifying mechanisms to address resulting plant stress, types of microbial inoculation to achieve desired outcomes, and co-producing plans of management with interest groups and rights holders. 

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3. Consumers stabilize grassland ecosystem functions by destabilizing belowground communities under abiotic stress

   https://doi.org/10.1002/ecy.70254  

   Lucas, Jane M; Budny, Michelle L; Lemoine, Nathan P (November 2025, Ecology)

   Abstract Consumers play a critical role in mediating plant and ecosystem responses to abiotic stress, yet their influence on belowground processes under changing environmental conditions remains underexplored. Insect consumers are vital components of grassland ecosystems that can shape ecosystem function and stability by mitigating how plant and microbial communities respond to abiotic stress, like drought. This study investigates how small‐bodied consumers influence the magnitude and stability of grassland belowground functions across gradients of abiotic stress. We conducted a fully factorial field experiment manipulating consumer presence and induced drought over a growing season. Our results reveal that the presence of consumers stabilizes bacterial biomass and microbial activity across variable soil moisture conditions. Interestingly, this consumer‐induced increase in ecosystem stability was driven by a destabilization of microbial communities, as indicated by increased variability in bacterial community composition and abundance. Consumer presence also shifted soil bacterial community composition and richness, while fungal communities were less affected. Combined, our results highlight another important dimension of ecosystem stability: community responsiveness and rapid adaptability. Additionally, our findings underscore the critical role of consumers in maintaining belowground ecosystem stability and highlight the need to consider trophic interactions when predicting the impacts of global change on grassland ecosystems. 

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4. Environmental stress destabilizes microbial networks

   https://doi.org/10.1038/s41396-020-00882-x  

   Hernandez, Damian J.; David, Aaron S.; Menges, Eric S.; Searcy, Christopher A.; Afkhami, Michelle E. (January 2021, The ISME Journal)

   Abstract Environmental stress is increasing worldwide, yet we lack a clear picture of how stress disrupts the stability of microbial communities and the ecosystem services they provide. Here, we present the first evidence that naturally-occurring microbiomes display network properties characteristic of unstable communities when under persistent stress. By assessing changes in diversity and structure of soil microbiomes along 40 replicate stress gradients (elevation/water availability gradients) in the Florida scrub ecosystem, we show that: (1) prokaryotic and fungal diversity decline in high stress, and (2) two network properties of stable microbial communities—modularity and negative:positive cohesion—have a clear negative relationship with environmental stress, explaining 51–78% of their variation. Interestingly, pathogenic taxa/functional guilds decreased in relative abundance along the stress gradient, while oligotrophs and mutualists increased, suggesting that the shift in negative:positive cohesion could result from decreasing negative:positive biotic interactions consistent with the predictions of the Stress Gradient Hypothesis. Given the crucial role microbiomes play in ecosystem functions, our results suggest that, by limiting the compartmentalization of microbial associations and creating communities dominated by positive associations, increasing stress in the Anthropocene could destabilize microbiomes and undermine their ecosystem services. 

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5. Rooting for function: community‐level fine‐root traits relate to many ecosystem functions

   https://doi.org/10.1111/nph.70606  

   Barry, Kathryn E; Hennecke, Justus; Weigelt, Alexandra; Bergmann, Joana; Bruelheide, Helge; Freschet, Grégoire T; Iversen, Colleen M; Kuyper, Thomas W; Laughlin, Daniel C; McCormack, M Luke; et al (October 2025, New Phytologist)

   Summary Humans are driving biodiversity change, which also alters community functional traits. However, how changes in the functional traits of the community alter ecosystem functions—especially belowground—remains an important gap in our understanding of the consequences of biodiversity change.We test hypotheses for how the root traits of the root economics space (composed of the collaboration and conservation gradients) are associated with proxies for ecosystem functioning across grassland and forest ecosystems in both observational and experimental datasets from 810 plant communities. First, we assessed whether community‐weighted means of the root economics space traits adhered to the same trade‐offs as species‐level root traits. Then, we examined the relationships between community‐weighted mean root traits and aboveground biomass production, root standing biomass, soil fauna biomass, soil microbial biomass, decomposition of standard and plot‐specific material, ammonification, nitrification, phosphatase activity, and drought resistance.We found evidence for a community collaboration gradient but not for a community conservation gradient. Yet, links between community root traits and ecosystem functions were more common than we expected, especially for aboveground biomass, microbial biomass, and decomposition.These findings suggest that changes in species composition, which alter root trait means, will in turn affect critical ecosystem functions. 

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