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1. Globally consistent response of plant microbiome diversity across hosts and continents to soil nutrients and herbivores

   https://doi.org/10.1038/s41467-023-39179-w  

   Seabloom, Eric W.; Caldeira, Maria C.; Davies, Kendi F.; Kinkel, Linda; Knops, Johannes M. H.; Komatsu, Kimberly J.; MacDougall, Andrew S.; May, Georgiana; Millican, Michael; Moore, Joslin L.; et al (June 2023, Nature Communications)

   Abstract All multicellular organisms host a diverse microbiome composed of microbial pathogens, mutualists, and commensals, and changes in microbiome diversity or composition can alter host fitness and function. Nonetheless, we lack a general understanding of the drivers of microbiome diversity, in part because it is regulated by concurrent processes spanning scales from global to local. Global-scale environmental gradients can determine variation in microbiome diversity among sites, however an individual host’s microbiome also may reflect its local micro-environment. We fill this knowledge gap by experimentally manipulating two potential mediators of plant microbiome diversity (soil nutrient supply and herbivore density) at 23 grassland sites spanning global-scale gradients in soil nutrients, climate, and plant biomass. Here we show that leaf-scale microbiome diversity in unmanipulated plots depended on the total microbiome diversity at each site, which was highest at sites with high soil nutrients and plant biomass. We also found that experimentally adding soil nutrients and excluding herbivores produced concordant results across sites, increasing microbiome diversity by increasing plant biomass, which created a shaded microclimate. This demonstration of consistent responses of microbiome diversity across a wide range of host species and environmental conditions suggests the possibility of a general, predictive understanding of microbiome diversity. 

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2. Wildfire impact on soil microbiome life history traits and roles in ecosystem carbon cycling

   https://doi.org/10.1093/ismeco/ycae108  

   Nelson, Amelia_R; Rhoades, Charles_C; Fegel, Timothy_S; Roth, Holly_K; Caiafa, Marcos_V; Glassman, Sydney_I; Borch, Thomas; Wilkins, Michael_J (August 2024, ISME Communications)

   Abstract Wildfires, which are increasing in frequency and severity with climate change, reduce soil microbial biomass and alter microbial community composition and function. The soil microbiome plays a vital role in carbon (C) and nitrogen (N) cycling, but its complexity makes it challenging to predict post-wildfire soil microbial dynamics and resulting impacts on ecosystem biogeochemistry. The application of biogeochemically relevant conceptual trait-based frameworks to the soil microbiome can distill this complexity, enabling enhanced predictability of soil microbiome recovery following wildfire and subsequent impacts to biogeochemical cycles. Conceptual frameworks that have direct links to soil C and N cycling have been developed for the soil microbiome; the Y-A-S framework overviews soil microbiome life history strategies that have tradeoffs with one another and others have proposed frameworks specific to wildfire. Here, we aimed to delineate post-wildfire changes of bacterial traits in western US coniferous forests to inform how severe wildfire influences soil microbiome recovery and resultant biogeochemical cycling. We utilized a comprehensive metagenome-assembled genome catalog from post-wildfire soils representing 1 to 11 years following low- and high-severity burning to identify traits that enable the persistence of microbial taxa in burned soils and influence ecosystem C and N cycling. We found that high-severity wildfire initially selects for fast growers and, up to a decade post-fire, taxa that invest in genes for acquiring diverse resources from the external environment, which in combination could increase soil C losses. This work begins to disentangle how climate change–induced shifts in wildfire behavior might alter microbially mediated soil biogeochemical cycling. 

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3. Microbiome‐mediated response to pulse fire disturbance outweighs the effects of fire legacy on plant performance

   https://doi.org/10.1111/nph.17689  

   Revillini, Daniel; David, Aaron S.; Menges, Eric S.; Main, Kevin N.; Afkhami, Michelle E.; Searcy, Christopher A. (September 2021, New Phytologist)

   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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4. Reciprocal microbiome transplants differentially rescue fitness in two syntopic dung beetle sister species (Scarabaeidae: Onthophagus )

   https://doi.org/10.1111/een.13031  

   Parker, Erik_S; Moczek, Armin_P; Macagno, Anna_L_M (March 2021, Ecological Entomology)

   1. Microbial symbionts play a crucial role in the development, health, and homeostasis of their hosts. However, the eco‐evolutionary conditions shaping these relationships and the evolutionary scale at which host–microbiome interactions may diverge warrant further investigation, especially in non‐model systems. This study examines the impact of reciprocal gut microbiome transplants between two ecologically very similar, sympatric, and syntopic dung beetle sister species. 2.Onthophagus vaccaandOnthophagus mediuswere specifically used to compare the growth, development, and fitness outcomes of individuals that were either (i) reared in the presence of a microbiome provided by a mother of the same species (“self‐inoculated”), (ii) forced to develop with a microbiome derived from a heterospecific mother (“cross‐inoculated”), or (iii) reared without a maternally transmitted microbiome. 3. This study found that individuals reared in the absence of a maternally derived gut microbiome incur detrimental changes in survival, as well as in several metrics signalling normative development. Furthermore, such negative effects are only partly rescued through inoculation with a heterologous microbiome. 4. Collectively, this study's results suggest that inoculation with a species‐specific, maternally transmitted microbiome is critical for normative development, that the significance of maternally derived microbiota for host survival differs across species, and that the phenotypic outcomes resulting from host–microbiome interactions may diverge even between closely related, ecologically similar host species. 

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5. Manipulating plant microbiomes in the field: Native mycorrhizae advance plant succession and improve native plant restoration

   https://doi.org/10.1111/1365-2664.14036  

   Koziol, Liz; Bauer, Jonathan T.; Duell, Eric B.; Hickman, Karen; House, Geoffrey L.; Schultz, Peggy A.; Tipton, Alice G.; Wilson, Gail W. T.; Bever, James D. (October 2021, Journal of Applied Ecology)

   Abstract The plant microbiome is critical to plant health and is degraded with anthropogenic disturbance. However, the value of re‐establishing the native microbiome is rarely considered in ecological restoration. Arbuscular mycorrhizal (AM) fungi are particularly important microbiome components, as they associate with most plants, and later successional grassland plants are strongly responsive to native AM fungi.With five separate sites across the United States, we inoculated mid‐ and late successional plant seedlings with one of three types of native microbiome amendments: (a) whole rhizosphere soil collected from local old‐growth, undisturbed grassland communities in Illinois, Kansas or Oklahoma, (b) laboratory cultured AM fungi from these same old‐growth grassland sites or (c) no microbiome amendment. We also seeded each restoration with a diverse native seed mixture. Plant establishment and growth was followed for three growing seasons.The reintroduction of soil microbiome from native ecosystems improved restoration establishment.Including only native arbuscular mycorrhizal fungal communities produced similar improvements in plant establishment as what was found with whole soil microbiome amendment. These findings were robust across plant functional groups.Inoculated plants (amended with either AM fungi or whole soil) also grew more leaves and were generally taller during the three growing seasons.Synthesis and applications. Our research shows that mycorrhizal fungi can accelerate plant succession and that the reintroduction of both whole soil and laboratory cultivated native mycorrhizal fungi can be used as tools to improve native plant restoration following anthropogenic disturbance. 

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