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1. Rhizosphere Microbiomes in a Historical Maize-Soybean Rotation System Respond to Host Species and Nitrogen Fertilization at the Genus and Subgenus Levels

   https://doi.org/10.1128/AEM.03132-20  

   Meier, Michael A.; Lopez-Guerrero, Martha G.; Guo, Ming; Schmer, Marty R.; Herr, Joshua R.; Schnable, James C.; Alfano, James R.; Yang, Jinliang (May 2021, Applied and Environmental Microbiology)

   Liu, Shuang-Jiang (Ed.)

   ABSTRACT Root-associated microbes are key players in plant health, disease resistance, and nitrogen (N) use efficiency. It remains largely unclear how the interplay of biological and environmental factors affects rhizobiome dynamics in agricultural systems. In this study, we quantified the composition of rhizosphere and bulk soil microbial communities associated with maize ( Zea mays L.) and soybean ( Glycine max L.) in a long-term crop rotation study under conventional fertilization and low-N regimes. Over two growing seasons, we evaluated the effects of environmental conditions and several treatment factors on the abundance of rhizosphere- and soil-colonizing microbial taxa. Time of sampling, host plant species, and N fertilization had major effects on microbiomes, while no effect of crop rotation was observed. Using variance partitioning as well as 16S sequence information, we further defined a set of 82 microbial genera and functional taxonomic groups at the subgenus level that show distinct responses to treatment factors. We identified taxa that are highly specific to either maize or soybean rhizospheres, as well as taxa that are sensitive to N fertilization in plant rhizospheres and bulk soil. This study provides insights to harness the full potential of soil microbes in maize and soybean agricultural systems through plant breeding and field management. IMPORTANCE Plant roots are colonized by large numbers of microbes, some of which may help the plant acquire nutrients and fight diseases. Our study contributes to a better understanding of root-colonizing microbes in the widespread and economically important maize-soybean crop rotation system. The long-term goal of this research is to optimize crop plant varieties and field management to create the best possible conditions for beneficial plant-microbe interactions to occur. These beneficial microbes may be harnessed to sustainably reduce dependency on pesticides and industrial fertilizer. We identify groups of microbes specific to the maize or to the soybean host and microbes that are sensitive to nitrogen fertilization. These microbes represent candidates that may be influenced through plant breeding or field management, and future research will be directed toward elucidating their roles in plant health and nitrogen usage. 

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2. Soil moisture incidentally selects for microbes that facilitate locally adaptive plant response

   https://doi.org/10.1098/rspb.2023.0469  

   Ricks, Kevin D.; Yannarell, Anthony C. (June 2023, Proceedings of the Royal Society B: Biological Sciences)

   While a plant's microbiome can facilitate adaptive phenotypes, the plant's role in selecting for these microbes is unclear. Do plants actively recruit microbes beneficial to their current environment, or are beneficial microbes only an incidental by-product of microbial adaptation? We addressed these questions through a multigeneration greenhouse experiment, selecting for either dry- or wet-adapted soil microbial communities, either with or without plants. After three plant generations, we conducted a full reciprocal transplant of each soil community onto wet- and dry-treated plants. We found that plants generally benefited from soil microbes, and this benefit was greater whenever their current watering conditions matched the microbes' historical watering conditions. Principally, the plant's presence was not necessary in the historical treatments for this environmental matching benefit to emerge. Moreover, we found microbes from droughted soils could better tolerate drought stress. Taken together, these results suggest that the moisture environment selects for microbes that benefit plants under those specific moisture conditions, and that these beneficial properties arise as a by-product of microbial adaptation to the watering environment and not as a co-adapting plant–microbe system. This work highlights that understanding the selective agents on these plant-associated microbes will lead to a better understanding of plant adaptation. 

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3. Soil microbes weaken the positive effect of an aquatic–terrestrial subsidy on plant performance

   https://doi.org/10.1093/jpe/rtaa079  

   Garcia, Alejandra B; Locke, Hannah; Crawford, Kerri M (February 2021, Journal of Plant Ecology)

   Hu, Shuijin (Ed.)

   Abstract Aims Linkages formed through aquatic–terrestrial subsidies can play an important role in structuring communities and mediating ecosystem functions. Aquatic–terrestrial subsidies may be especially important in nutrient-poor ecosystems, such as the freshwater sand dunes surrounding Lake Michigan. Adult midges emerge from Lake Michigan in the spring, swarm to mate and die. Their carcasses form mounds at the base of plants, where they may increase plant productivity through their nutrient inputs. However, the effect of aquatic–terrestrial subsidies on plant productivity could depend on other biotic interactions. In particular, soil microbes might play a key role in facilitating the conversion of nutrients to plant-available forms or competing for the nutrients with plants. Methods In a greenhouse experiment, we tested how carcasses from lake emergent midges (Chironomidae) and soil microbes independently and interactively influenced the performance of a common dune grass, Calamovilfa longifolia. To determine whether midges influenced abiotic soil properties, we measured how midge additions influenced soil nutrients and soil moisture. Important Findings Midges greatly increased plant biomass, while soil microbes influenced the magnitude of this effect. In the absence of soil microbes plant biomass was seven times greater with midges than without midges. However, in the presence of soil microbes, plant biomass was only three times greater. The effect of midges might be driven by their nutrient inputs into the soil, as midges contained 100 times more N, 10 times more P and 150 times more K than dune soils did. Our results suggest that soil microbes may be competing with plants for these nutrients. In sum, we found that midges can be an important aquatic–terrestrial subsidy that produces strong, positive effects on plant productivity along the shorelines of Lake Michigan, but that the impact of aquatic–terrestrial subsidies must be considered within the context of the complex interactions that take place within ecological communities. 

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4. Native Microbes Amplify Native Seedling Establishment and Diversity While Inhibiting a Non-Native Grass

   https://doi.org/10.3390/plants12051184  

   Koziol, Liz; McKenna, Thomas P.; Bever, James D. (March 2023, Plants)

   Although several studies have shown increased native plant establishment with native microbe soil amendments, few studies have investigated how microbes can alter seedling recruitment and establishment in the presence of a non-native competitor. In this study, the effect of microbial communities on seedling biomass and diversity was assessed by seeding pots with both native prairie seeds and a non-native grass that commonly invades US grassland restorations, Setaria faberi. Soil in the pots was inoculated with whole soil collections from ex-arable land, late successional arbuscular mycorrhizal (AM) fungi isolated from a nearby tallgrass prairie, with both prairie AM fungi and ex-arable whole soil, or with a sterile soil (control). We hypothesized (1) late successional plants would benefit from native AM fungi, (2) that non-native plants would outcompete native plants in ex-arable soils, and (3) early successional plants would be unresponsive to microbes. Overall, native plant abundance, late successional plant abundance, and total diversity were greatest in the native AM fungi+ ex-arable soil treatment. These increases led to decreased abundance of the non-native grass S. faberi. These results highlight the importance of late successional native microbes on native seed establishment and demonstrate that microbes can be harnessed to improve both plant community diversity and resistance to invasion during the nascent stages of restoration. 

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5. Soil microbes influence the ecology and evolution of plant plasticity

   https://doi.org/10.1111/nph.20383  

   Bolin, Lana G (March 2025, New Phytologist)

   Summary Stress often induces plant trait plasticity, and microbial communities also alter plant traits. Therefore, it is unclear how much plasticity results from direct plant responses to stress vs indirect responses due to stress‐induced changes in soil microbial communities.To test how microbes and microbial community responses to stress affect the ecology and potentially the evolution of plant plasticity, I grew plants in four stress environments (salt, herbicide, herbivory, and no stress) with microbes that had responded to these same environments or with sterile inoculant.Plants delayed flowering under stress only when inoculated with live microbial communities, and this plasticity was maladaptive. However, microbial communities responded to stress in ways that accelerated flowering across all environments. Microbes also affected the expression of genetic variation for plant flowering time and specific leaf area, as well as genetic variation for plasticity of both traits, and disrupted a positive genetic correlation for plasticity in response to herbicide and herbivory stress, suggesting that microbes may affect the pace of plant evolution.Together, these results highlight an important role for soil microbes in plant plastic responses to stress and suggest that microbes may alter the evolution of plant plasticity. 

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