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1. Residence Time Structures Microbial Communities Through Niche Partitioning

   https://doi.org/10.1111/ele.70093  

   Mueller, Emmi A; Lennon, Jay T (February 2025, Ecology Letters)

   ABSTRACT Much of life on Earth is at the mercy of currents and flow. Residence time (τ) estimates how long organisms and resources remain in a system based on the ratio of volume (V) to flow rate (Q). Shortτshould promote immigration but limit species establishment, while longτshould favour species that survive on limited resources. Theory suggests these opposing forces shape the abundance, diversity and function of flowing systems. We experimentally tested how residence time affects a lake microbial community by exposing chemostats to aτgradient spanning seven orders of magnitude. Microbial abundance, richness and evenness increased non‐linearly withτ, while functions like productivity and resource consumption declined. Taxa formed distinct clusters of short‐ and long‐τspecialists consistent with niche partitioning. Our findings demonstrate that residence time drives biodiversity and community function in flowing habitats that are commonly found in environmental, engineered and host‐associated ecosystems. 

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2. Growth characteristics of natural microbial populations are skewed toward bacteria with low specific growth rates

   https://doi.org/10.1128/spectrum.02193-26  

   Bulseco, Ashley N; Yang, Wenzhuo; Huber, Julie A; Vallino, Joseph J (August 2026, Microbiology Spectrum)

   Steven, Blaire (Ed.)

   ABSTRACT Microbes are often functionally characterized by traits that specify their optimum environmental conditions for growth, such as temperature or pH, as well as upper and lower bounds where growth is possible. While any given microbe will have a narrow environmental window where growth can occur, a diverse community can span a much larger range of conditions where growth is possible by at least some members of the community. One important trait of microbes is maximum specific growth rate, as this trait determines if a microbe can persist in environments with short residence times. In this study, we conducted a chemostat experiment with natural microbial communities and manipulated dilution rate to test how it would act as a selective force controlling community dynamics and microbial diversity. Using both the experimental chemostats, as well as trait-based modeling, we examined how the composition of a microbial community collected from a coastal meromictic pond changed as dilution rate increased from 0.1 to 10 day⁻¹. We compared experimental results from 16S rRNA gene amplicon sequences to the output from two different simulations of the trait-based model, one in which maximum specific growth rate was initially evenly distributed across the community, and another where maximum specific growth rate traits were pulled from a beta probability distribution that was skewed toward low specific growth rates. Experimental results matched the simulation where the initial natural population was dominated by slow-growing microbes, highlighting the importance of initial trait distributions in modeling community response to environmental changes.IMPORTANCEAll living organisms are constrained by environmental boundaries that govern where growth is possible, such as minimum and maximum temperatures or pH. An organism’s maximum specific growth rate places a lower bound on the residence or turnover time where an organism can persist without being removed from the system. While there are laboratory constraints on the maximum specific growth rate of culturable microorganisms, such asEscherichiaorVibriospecies, information is lacking on how the maximum specific growth rate trait is distributed in natural microbial communities. This information is critical for understanding how a community will respond to changes in residence time or other environmental perturbations. Using chemostats and trait-based modeling, this study assessed how maximum specific growth rate is distributed in a natural community collected from a coastal, salinity-stratified pond. 

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3. Organic and inorganic fertilizers modulate the response of the soil microbiome to salinity stress

   https://doi.org/10.3389/fmicb.2025.1551586  

   Malal, Halima; Garcia, Joshua A; Marrs, Anna; Ait_Hamza, Mohamed; Emerson, Courtney; Nocco, Mallika; Lakhtar, Hicham; Lazcano, Cristina (June 2025, Frontiers in Microbiology)

   Salinity stress threatens soil microbiomes, a key driver of soil multifunctionality and health. This study employed high-throughput sequencing of 16S rRNA, PLFAs, multifunctionality index, and co-occurrence networks to gain a comprehensive understanding of the dynamic responses of soil microbiomes to salinity stress gradient (0, 0.4 and 1 mol NaCl). Additionally, we investigated how these responses are shaped by the addition of vermicompost and NPK fertilizer during short-term (2-h) and long-term (70-day) incubation periods. Salinity stress reduced bacterial and fungal phospholipid fatty acids (PLFA) concentrations in the short-term. Over the long-term, the microbial community evolved into a new pattern under salt stress, favoring the presence ofBacteriodota, a salt-tolerant phylum, while decreasing the relative abundance ofAcidobacteriotaandPlanctomycetota, which are more salt-sensitive. Furthermore, salinity decreased species richness by 11.33% and soil multifunctionality by 21.48% but increased microbial network complexity while decreasing its stability. Incorporating vermicompost increased bacterial and fungal PLFAs, enhanced bacterial diversity by 2.33%, promoted salt-tolerant bacteria, and increased the complexity and stability of the bacterial network. Conversely, the application of NPK fertilizer reduced bacterial richness, alpha diversity and soil multifunctionality by 14.52, 5.83, and 12.34%, respectively, further disrupting the microbial community and making resilience to salinity stress more challenging. Furthermore, NPK fertilization increased bacterial network complexity but decreased its stability. This study underscores the significance of employing vermicompost to improve the health of saline soils. Furthermore, it emphasizes the negative impacts of NPK fertilizer on soil microbial structure and function and hinder its recovery from salinity’s impacts. 

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4. Hydrology drives facilitative and competitive strategies in freshwater macrophyte and microbial communities

   https://doi.org/10.1002/ecs2.70384  

   Kleindl, Paige M; Wachnicka, Anna; Sah, Jay P; Ross, Michael S; Gaiser, Evelyn E (September 2025, Ecosphere)

   Abstract Pulses of resource availability along environmental gradients can filter the local and regional distribution of macrophyte and microbial mat communities in wetlands. Wetlands that experience short hydroperiods (i.e., <6 months with standing water) may cause macrophyte and microbial mat competition for water. However, the stress gradient hypothesis predicts that abiotic stress should increase facilitative co‐regulation of producer dynamics. To determine if and how macrophyte and microbial mat biomass covary along a hydrologic gradient, we conducted two observational surveys and a biomass removal experiment in Everglades National Park, FL, USA. In the survey, macrophyte and microbial mat biomass were measured over a two‐year period across nine hydrologically regulated macrophyte community types to determine drivers of biomass and macrophyte–microbial mat interactions along a hydroperiod gradient (3–8 months) using a structural equation model. In the experiment, the effect of hydrology on the interaction between macrophytes and microbial mats was quantified by measuring the effect of bimonthly removal of macrophyte or microbial mat biomass on the biomass of both communities in plots in wetlands with contrasting hydroperiods (3–6 months). Hydrology and biological interactions influenced macrophyte and microbial mat biomass, with stronger interactions observed in the shortest hydroperiod transect sites dominated bySchoenus nigricansandCladium jamaicense. Along the hydrologic gradient, we found direct negative effects of macrophyte biomass on microbial biomass and vice versa, and a significant positive effect of microbial response to flooding duration on macrophyte biomass. Experimental macrophyte removal in shorter‐hydroperiod wetlands resulted in a significant increase in microbial biomass while microbial mat removal reduced biomass of the dominant macrophyteC. jamaicense. The facilitative effect of microbial mats on macrophyte biomass in shorter‐hydroperiod wetlands may be driven by mats prolonging soil moisture retention due to their desiccation‐resistant structure. Stress‐induced facilitation supported the stress gradient hypothesis across the short‐hydrologic gradient, while competitive interactions were also observed. As climate and human drivers continue altering hydrology in aquatic systems, the type and strength of community interactions will continue to shift and alter distributions across the landscape. 

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5. A Quantitative Classification of the Geography of Non‐Native Flora in the United States

   https://doi.org/10.1111/geb.70041  

   Bradley, Bethany A; Evans, Annette E; Sofaer, Helen R; Vilà, Montserrat; Barnett, David T; Beaury, Evelyn M; Blumenthal, Dana M; Corbin, Jeffrey D; Dukes, Jeffrey S; Early, Regan; et al (April 2025, Global Ecology and Biogeography)

   ABSTRACT AimNon‐native plants have the potential to harm ecosystems. Harm is classically related to their distribution and abundance, but this geographical information is often unknown. Here, we assess geographical commonness as a potential indicator of invasive status for non‐native flora in the United States. Geographical commonness could inform invasion risk assessments across species and ecoregions. LocationConterminous United States. Time PeriodThrough 2022. Major Taxa StudiedPlants. MethodsWe compiled and standardised occurrence and abundance data from 14 spatial datasets and used this information to categorise non‐native species as uncommon or common based on three dimensions of commonness: area of occupancy, habitat breadth and local abundance. To assess consistency in existing categorizations, we compared commonness to invasive status in the United States. We identified species with higher‐than‐expected abundance relative to their occupancy, habitat breadth or residence time. We calculated non‐native plant richness within United States ecoregions and estimated unreported species based on rarefaction/extrapolation curves. ResultsThis comprehensive database identified 1874 non‐native plant species recorded in 4,844,963 locations. Of these, 1221 species were locally abundant (> 10% cover) in 797,759 unique locations. One thousand one hundred one non‐native species (59%) achieved at least one dimension of commonness, including 565 species that achieved all three. Species with longer residence times tended to meet more dimensions of commonness. We identified 132 species with higher‐than‐expected abundance. Ecoregions in the central United States have the largest estimated numbers of unreported, abundant non‐native plants. Main ConclusionsA high proportion of non‐native species have become common in the United States. However, existing categorizations of invasive species are not always consistent with species' abundance and distribution, even after considering residence time. Considering geographical commonness and higher‐than‐expected abundance revealed in this new dataset could support more consistent and proactive identification of invasive plants and lead to more efficient management practices. 

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