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  1. Habitat specialization underpins biological processes from species distributions to speciation. However, organisms are often described as specialists or generalists based on a single niche axis, despite facing complex, multidimensional environments. Here, we analysed 236 environmental soil microbiomes across the United States and demonstrate that 90% of >1,200 prokaryotes followed one of two trajectories: specialization on all niche axes (multidimensional specialization) or generalization on all axes (multidimensional generalization). We then documented that this pervasive multidimensional specialization/generalization had many ecological and evolutionary consequences. First, multidimensional specialization and generalization are highly conserved with very few transitions between these two trajectories. Second, multidimensional generalists dominated communities because they were 73 times more abundant than specialists. Lastly, multidimensional specialists played important roles in community structure with ~220% more connections in microbiome networks. These results indicate that multidimensional generalization and specialization are evolutionarily stable with multidimensional generalists supporting larger populations and multidimensional specialists playing important roles within communities, probably stemming from their overrepresentation among pollutant detoxifiers and nutrient cyclers. Taken together, we demonstrate that the vast majority of soil prokaryotes are restricted to one of two multidimensional niche trajectories, multidimensional specialization or multidimensional generalization, which then has far-reaching consequences for evolutionary transitions, microbial dominance and community roles. 
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    Free, publicly-accessible full text available September 1, 2024
  2. Abstract

    Improved understanding of bacterial community responses to multiple environmental filters over long time periods is a fundamental step to develop mechanistic explanations of plant–bacterial interactions as environmental change progresses.

    This is the first study to examine responses of grassland root‐associated bacterial communities to 15 years of experimental manipulations of plant species richness, functional group and factorial enrichment of atmospheric CO2(eCO2) and soil nitrogen (+N).

    Across the experiment, plant species richness was the strongest predictor of rhizobacterial community composition, followed by +N, with no observed effect of eCO2. Monocultures of C3and C4grasses and legumes all exhibited dissimilar rhizobacterial communities within and among those groups. Functional responses were also dependent on plant functional group, where N2‐fixation genes, NO3−‐reducing genes and P‐solubilizing predicted gene abundances increased under resource‐enriched conditions for grasses, but generally declined for legumes. In diverse plots with 16 plant species, the interaction of eCO2+N altered rhizobacterial composition, while +N increased the predicted abundance of nitrogenase‐encoding genes, and eCO2+N increased the predicted abundance of bacterial P‐solubilizing genes.

    Synthesis: Our findings suggest that rhizobacterial community structure and function will be affected by important global environmental change factors such as eCO2, but these responses are primarily contingent on plant species richness and the selective influence of different plant functional groups.

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  3. Summary

    Allelopathy is a common and important stressor that shapes plant communities and can alter soil microbiomes, yet little is known about the direct effects of allelochemical addition on bacterial and fungal communities or the potential for allelochemical‐selected microbiomes to mediate plant performance responses, especially in habitats naturally structured by allelopathy.

    Here, we present the first community‐wide investigation of microbial mediation of allelochemical effects on plant performance by testing how allelopathy affects soil microbiome structure and how these microbial changes impact germination and productivity across 13 plant species.

    The soil microbiome exhibited significant changes to ‘core’ bacterial and fungal taxa, bacterial composition, abundance of functionally important bacterial and fungal taxa, and predicted bacterial functional genes after the addition of the dominant allelochemical native to this habitat. Furthermore, plant performance was mediated by the allelochemical‐selected microbiome, with allelopathic inhibition of plant productivity moderately mitigated by the microbiome.

    Through our findings, we present a potential framework to understand the strength of plant–microbial interactions in the presence of environmental stressors, in which frequency of the ecological stress may be a key predictor of microbiome‐mediation strength.

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  4. Summary

    Fire plays a major role in structuring plant communities across the globe. Interactions with soil microbes impact plant fitness, scaling up to influence plant populations and distributions. Here we present the first factorial manipulation of both fire and soil microbiome presence to investigate their interactive effects on plant performance across a suite of plant species with varying life history traits.

    We conducted fully factorial experiments on 11 species from the Florida scrub ecosystem to test plant performance responses to soils with varying fire histories (36 soil sources), the presence/absence of a microbiome, and exposure to an experimental burn.

    Results revealed interactive ‘pulse’ effects between fire and the soil microbiome on plant performance. On average, post‐fire soil microbiomes strongly reduced plant productivity compared to unburned or sterilized soils. Interestingly, longer‐term fire ‘legacy’ effects had minor impacts on plant performance and were unrelated to soil microbiomes.

    While pulse fire effects on plant–microbiome interactions are short‐term, they could have long‐term consequences for plant communities by establishing differential microbiome‐mediated priority effects during post‐disturbance succession. The prominence of pulse fire effects on plant–microbe interactions has even greater import due to expected increases in fire disturbances resulting from anthropogenic climate change.

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