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1. Microbial ecology for all: A vision of accessibility, unity, and responsibility

   https://doi.org/10.1002/ecy.70342  

   Sorouri, Bahareh; Bernardin, Jessica; Favier, Ariel Ignacio; Garces, Kylea Rose; McMullen, John George; McGuire, Rosa Maria (March 2026, Ecology)

   Abstract Microorganisms are ubiquitous in nature, representing a significant portion of global biodiversity and playing vital roles in ecosystem functions, biogeochemical cycles, and organismal health. The growing recognition of microbial importance and their potential to address ecological and global challenges has inspired a renewed interest and innovation in microbial ecology. This field has benefited immensely from sequencing technologies that allow scientists to explore diversity at scales previously unimaginable. While the rapid growth of the field has offered significant positive advancements and foreshadows promising potential, there are aspects that need careful consideration. New technology has led to exponential growth in available microbial data, yet not everyone has easy access to sequencing technology, data mining and analysis tools, or the time to acquire new skills. Thus, we are at a crossroads in ensuring that these resources are accessible for all, and that traditional methods of microbiology are still appreciated as tools to progress the field in meaningful ways. As early‐career researchers, we want to raise these points as principles for shaping the future of microbial ecology. Here, we outline a vision for a more accessible, united, and responsible microbial ecology field, one with applications equipped to address the needs of both society and the environment. To democratize the field, we advocate to destigmatize microbes and increase awareness of their beneficial roles by integrating microbes into early education. We believe unity and collaboration among microbial ecologists, as well as with professionals and community members in other STEM fields, are essential for advancing the field. Data should be accessible and standardized for collaboration, and greater integration across disciplines is essential to address future ecological challenges effectively and innovatively. It is our responsibility to ensure that we are asking relevant research questions with the potential to engage with socio‐environmental issues and prioritize sustainable practices. As a collective field, our research should strive to not only expand scientific knowledge but also support community resilience and policy‐making for a sustainable future. Together, this vision will promote a more equitable, diverse, and collaborative future for microbial ecology; and has applications for the broader ecology field. 

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2. Warming alters cascading effects of a dominant arthropod predator on fungal community composition in the Arctic

   https://doi.org/10.1128/mbio.00590-24  

   Koltz, Amanda M; Koyama, Akihiro; Wallenstein, Matthew (July 2024, mBio)

   Giovannoni, Stephen J; Weedon, James (Ed.)

   ABSTRACT Rapid climate change in the Arctic is altering microbial structure and function, with important consequences for the global ecosystem. Emerging evidence suggests organisms in higher trophic levels may also influence microbial communities, but whether warming alters these effects is unclear. Wolf spiders are dominant Arctic predators whose densities are expected to increase with warming. These predators have temperature-dependent effects on decomposition via their consumption of fungal-feeding detritivores, suggesting they may indirectly affect the microbial structure as well. To address this, we used a fully factorial mesocosm experiment to test the effects of wolf spider density and warming on litter microbial structure in Arctic tundra. We deployed replicate litter bags at the surface and belowground in the organic soil profile and analyzed the litter for bacterial and fungal community structure, mass loss, and nutrient characteristics after 2 and 14 months. We found there were significant interactive effects of wolf spider density and warming on fungal but not bacterial communities. Specifically, higher wolf spider densities caused greater fungal diversity under ambient temperature but lower fungal diversity under warming at the soil surface. We also observed interactive treatment effects on fungal composition belowground. Wolf spider density influenced surface bacterial composition, but the effects did not change with warming. These findings suggest a widespread predator can have indirect, cascading effects on litter microbes and that effects on fungi specifically shift under future expected levels of warming. Overall, our study highlights that trophic interactions may play important, albeit overlooked, roles in driving microbial responses to warming in Arctic terrestrial ecosystems. IMPORTANCEThe Arctic contains nearly half of the global pool of soil organic carbon and is one of the fastest warming regions on the planet. Accelerated decomposition of soil organic carbon due to warming could cause positive feedbacks to climate change through increased greenhouse gas emissions; thus, changes in ecological dynamics in this region are of global relevance. Microbial structure is an important driver of decomposition and is affected by both abiotic and biotic conditions. Yet how activities of soil-dwelling organisms in higher trophic levels influence microbial structure and function is unclear. In this study, we demonstrate that predicted changes in abundances of a dominant predator and warming interactively affect the structure of litter-dwelling fungal communities in the Arctic. These findings suggest predators may have widespread, indirect cascading effects on microbial communities, which could influence ecosystem responses to future climate change. 

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3. Observing weak adaptation of duckweeds to their local microbiome depends on local pondwater

   https://doi.org/10.1002/ajb2.70165  

   Rose, Ava M; O'Brien, Anna M (March 2026, American Journal of Botany)

   Abstract PremisePopulations can locally adapt to the biotic and abiotic factors of environments. However, detecting adaptation to biotic factors can depend on the abiotic conditions in which the adaptation is tested, and vice versa. The microbiome is one important aspect of the biotic environment: Interactions between microbiomes and their hosts are critical for host fitness and trait expression. If hosts adapt to local microbiomes, they may therefore depend on interactions with local microbes to express trait values adapted to the local abiotic environment. MethodsUsingLemna minor(duckweed) as a model host, we examined differences in host fitness when grown in local and nonlocal microbiomes and in local and nonlocal water. We experimentally recombined duckweeds, microbes, and water from four ponds around Durham, New Hampshire (United States) in well‐plate microcosms in a growth chamber. ResultsThe source of duckweeds, microbes, and water all affected microbial growth, duckweed growth, and duckweed traits. However, weak, marginally significant local adaptation resulted in higher frond area only when duckweeds were paired with their local water and local microbes. Microbial growth was also marginally reduced when duckweeds were paired with microbes and water from their local site. ConclusionsWhile microbiome impacts on duckweed growth and traits varied across abiotic contexts, local microbiomes provided only limited growth benefits. Harnessing the effects of plant microbiomes is an exciting area of applied research. Despite our findings, bioprospecting in local microbiomes could still be fruitful: It may be ecologically safer, and other plants may locally adapt to microbiomes. 

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4. Using simulated wildland fire to assess microbial survival at multiple depths from biocrust and bare soils

   https://doi.org/10.3389/fmicb.2023.1123790  

   Palmer, Brianne; Pietrasiak, Nicole; Cobb, Polina; Lipson, David (March 2023, Frontiers in Microbiology)

   IntroductionSurface soil microbial communities are directly exposed to the heat from wildland fires. Due to this, the microbial community composition may be stratified within the soil profile with more heat tolerant microbes near the surface and less heat tolerant microbes, or mobile species found deeper in the soil. Biological soil crusts, biocrusts, are found on the soil surface and contain a diverse microbial community that is directly exposed to the heat from wildland fires. MethodsHere, we used a simulated fire mesocosm along with a culture-based approach and molecular characterization of microbial isolates to understand the stratification of biocrust and bare soil microbes after low severity (450°C) and high severity (600°C) fires. We cultured and sequenced microbial isolates from 2 to 6 cm depth from both fire types. ResultsThe isolates were stratified along the soil depth. Green algal isolates were less thermotolerant and found in the deeper depths (4–6 cm) and the control soils, while several cyanobacteria in Oscillatoriales, Synechococcales, and Nostocales were found at 2–3 cm depth for both fire temperatures. An Alphaproteobacteria isolate was common across several depths, both fire types, and both fire temperatures. Furthermore, we used RNA sequencing at three depths after the high severity fire and one control to determine what microbial community is active following a fire. The community was dominated by Gammaproteobacteria, however some Cyanobacteria ASVs were also present. DiscussionHere we show evidence of stratification of soil and biocrust microbes after a fire and provide evidence that these microbes are able to survive the heat from the fire by living just below the soil surface. This is a steppingstone for future work on the mechanisms of microbial survival after fire and the role of soil insulation in creating resilient communities. 

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5. Decline of a distinct coral reef holobiont community under ocean acidification

   https://doi.org/10.1186/s40168-023-01683-y  

   Williams, Jake; Pettorelli, Nathalie; Hartmann, Aaron C; Quinn, Robert A; Plaisance, Laetitia; O’Mahoney, Michael; Meyer, Chris P; Fabricius, Katharina E; Knowlton, Nancy; Ransome, Emma (December 2024, Microbiome)

   Abstract BackgroundMicrobes play vital roles across coral reefs both in the environment and inside and upon macrobes (holobionts), where they support critical functions such as nutrition and immune system modulation. These roles highlight the potential ecosystem-level importance of microbes, yet most knowledge of microbial functions on reefs is derived from a small set of holobionts such as corals and sponges. Declining seawater pH — an important global coral reef stressor — can cause ecosystem-level change on coral reefs, providing an opportunity to study the role of microbes at this scale. We use an in situ experimental approach to test the hypothesis that under such ocean acidification (OA), known shifts among macrobe trophic and functional groups may drive a general ecosystem-level response extending across macrobes and microbes, leading to reduced distinctness between the benthic holobiont community microbiome and the environmental microbiome. ResultsWe test this hypothesis using genetic and chemical data from benthic coral reef community holobionts sampled across a pH gradient from CO₂seeps in Papua New Guinea. We find support for our hypothesis; under OA, the microbiome and metabolome of the benthic holobiont community become less compositionally distinct from the sediment microbiome and metabolome, suggesting that benthic macrobe communities are colonised by environmental microbes to a higher degree under OA conditions. We also find a simplification and homogenisation of the benthic photosynthetic community, and an increased abundance of fleshy macroalgae, consistent with previously observed reef microbialisation. ConclusionsWe demonstrate a novel structural shift in coral reefs involving macrobes and microbes: that the microbiome of the benthic holobiont community becomes less distinct from the sediment microbiome under OA. Our findings suggest that microbialisation and the disruption of macrobe trophic networks are interwoven general responses to environmental stress, pointing towards a universal, undesirable, and measurable form of ecosystem change. 

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