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  1. Abstract Background

    Root and soil microbial communities constitute the below-ground plant microbiome, are drivers of nutrient cycling, and affect plant productivity. However, our understanding of their spatiotemporal patterns is confounded by exogenous factors that covary spatially, such as changes in host plant species, climate, and edaphic factors. These spatiotemporal patterns likely differ across microbiome domains (bacteria and fungi) and niches (root vs. soil).


    To capture spatial patterns at a regional scale, we sampled the below-ground microbiome of switchgrass monocultures of five sites spanning > 3 degrees of latitude within the Great Lakes region. To capture temporal patterns, we sampled the below-ground microbiome across the growing season within a single site. We compared the strength of spatiotemporal factors to nitrogen addition determining the major drivers in our perennial cropping system. All microbial communities were most strongly structured by sampling site, though collection date also had strong effects; in contrast, nitrogen addition had little to no effect on communities. Though all microbial communities were found to have significant spatiotemporal patterns, sampling site and collection date better explained bacterial than fungal community structure, which appeared more defined by stochastic processes. Root communities, especially bacterial, were more temporally structured than soil communities which were more spatially structured,more »both across and within sampling sites. Finally, we characterized a core set of taxa in the switchgrass microbiome that persists across space and time. These core taxa represented < 6% of total species richness but > 27% of relative abundance, with potential nitrogen fixing bacteria and fungal mutualists dominating the root community and saprotrophs dominating the soil community.


    Our results highlight the dynamic variability of plant microbiome composition and assembly across space and time, even within a single variety of a plant species. Root and soil fungal community compositions appeared spatiotemporally paired, while root and soil bacterial communities showed a temporal lag in compositional similarity suggesting active recruitment of soil bacteria into the root niche throughout the growing season. A better understanding of the drivers of these differential responses to space and time may improve our ability to predict microbial community structure and function under novel conditions.

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  2. Abstract

    Cellulosic bioenergy is a primary land‐based climate mitigation strategy, with soil carbon (C) storage and nitrogen (N) conservation as important mitigation elements. Here, we present 13 years of soil C and N change under three cellulosic cropping systems: monoculture switchgrass (Panicum virgatumL.), a five native grasses polyculture, and no‐till corn (Zea maysL.). Soil C and N fractions were measured four times over 12 years. Bulk soil C in the 0–25 cm depth at the end of the study period ranged from 28.4 (± 1.4 se) Mg C ha−1in no‐till corn, to 30.8 (± 1.4) Mg C ha−1in switchgrass, and to 34.8 (± 1.4) Mg C ha−1in native grasses. Mineral‐associated organic matter (MAOM) ranged from 60% to 90% and particulate organic matter (POM) from 10% to 40% of total soil C. Over 12 years, total C as well as both C fractions persisted under no‐till corn and switchgrass and increased under native grasses. In contrast, POM N stocks decreased 33% to 45% across systems, whereas MAOM N decreased only in no‐till corn and by less than 13%. Declining POM N stocks likely reflect pre‐establishment land use, which included alfalfa and manure in earlier rotations. Root production and large soil aggregate formation explained 69% (p < 0.001)more »and 36% (p = 0.024) of total soil C change, respectively, and 60% (p = 0.020) and 41% (p = 0.023) of soil N change, demonstrating the importance of belowground productivity and soil aggregates for producing and protecting soil C and conserving soil N. Differences between switchgrass and native grasses also indicate a dependence on plant diversity. Soil C and N benefits of bioenergy crops depend strongly on root productivity and pre‐establishment land use.

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  3. Abstract

    Microorganisms can help plants and animals contend with abiotic stressors, but why they provide such benefits remains unclear. Here we investigated byproduct benefits, which occur when traits that increase the fitness of one species provide incidental benefits to another species with no direct cost to the provider. In a greenhouse experiment, microbial traits predicted plant responses to soil moisture such that bacteria with self‐beneficial traits in drought increased plant early growth, size at reproduction, and chlorophyll concentration under drought, while bacteria with self‐beneficial traits in well‐watered environments increased these same plant traits in well‐watered soils. Thus, microbial traits that promote microbial success in different moisture environments also promote plant success in these same environments. Our results demonstrate that byproduct benefits, a concept developed to explain the evolution of cooperation in pairwise mutualisms, can also extend to interactions between plants and nonsymbiotic soil microbes.

    Free, publicly-accessible full text available October 8, 2023
  4. Abstract

    Biological invasions are usually examined in the context of their impacts on native species. However, few studies have examined the dynamics between invaders when multiple exotic species successfully coexist in a novel environment. Yet, long‐term coexistence of now established exotic species has been observed in North American lady beetle communities. Exotic lady beetlesHarmonia axyridisandCoccinella septempunctatawere introduced for biological control in agricultural systems and have since become dominant species within these communities. In this study, we investigated coexistence via spatial and temporal niche partitioning amongH. axyridisandC. septempunctatausing a 31‐year data set from southwestern Michigan, USA. We found evidence of long‐term coexistence through a combination of small‐scale environmental, habitat, and seasonal mechanisms. Across years,H. axyridisandC. septempunctataexperienced patterns of cyclical dominance likely related to yearly variation in temperature and precipitation. Within years, populations ofC. septempunctatapeaked early in the growing season at 550 degree days, whileH. axyridispopulations grew in the season until 1250 degree days and continued to have high activity after this point.C. septempunctatawas generally most abundant in herbaceous crops, whereasH. axyridisdid not display strong habitat preferences. These findings suggest that within this regionH. axyridishas broader habitat and abiotic environmental preferences, whereasC. septempunctatathrives under more specific ecological conditions. These ecological differences havemore »contributed to the continued coexistence of these two invaders. Understanding the mechanisms that allow for the coexistence of dominant exotic species contributes to native biodiversity conservation management of invaded ecosystems.

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  5. abstract

    Long-term observations and experiments in diverse drylands reveal how ecosystems and services are responding to climate change. To develop generalities about climate change impacts at dryland sites, we compared broadscale patterns in climate and synthesized primary production responses among the eight terrestrial, nonforested sites of the United States Long-Term Ecological Research (US LTER) Network located in temperate (Southwest and Midwest) and polar (Arctic and Antarctic) regions. All sites experienced warming in recent decades, whereas drought varied regionally with multidecadal phases. Multiple years of wet or dry conditions had larger effects than single years on primary production. Droughts, floods, and wildfires altered resource availability and restructured plant communities, with greater impacts on primary production than warming alone. During severe regional droughts, air pollution from wildfire and dust events peaked. Studies at US LTER drylands over more than 40 years demonstrate reciprocal links and feedbacks among dryland ecosystems, climate-driven disturbance events, and climate change.

  6. Abstract

    Increasing the resilience of agricultural landscapes requires fundamental changes to the dominant commodity production model, including incorporating practices such as reduced tillage, cover cropping, and extended rotations that reduce soil disturbance while increasing biological diversity. Increasing farmer adoption of these conservation systems offers the potential to transform agriculture to a more vibrant, resilient system that protects soil, air, and water quality. Adoption of these resilience practices is not without significant challenges. This paper presents findings from a participatory effort to better understand these challenges and to develop solutions to help producers overcome them. Through repeated, facilitated discussions with farmers and agricultural and conservation professionals across the U.S. state of Michigan, we confronted the policy, economic, and structural barriers that are inhibiting broader adoption of conservation systems, as well as identified policies, programs, and markets that can support their adoption. What emerged was a complex picture and dynamic set of challenges at multiple spatial scales and across multiple domains. The primary themes emerging from these discussions were barriers and opportunities, including markets, social networks, human capital, and conservation programs. Exacerbating the technical, agronomic, and economic challenges farmers face at the farm level, there are a host of community constraints, marketmore »access and availability problems, climatic and environmental changes, and policies (governmental and corporate) that cross‐pressure farmers when it comes to making conservation decisions. Understanding these constraints is critical to developing programs, policies, and state and national investments that can drive adoption of conservation agriculture.

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  7. Abstract

    Soil moisture is a major driver of microbial activity and thus, of the release of carbon (C) into the Earth's atmosphere. Yet, there is no consensus on the relationship between soil moisture and microbial respiration, and as a result, moisture response functions are a poorly constrained aspect of C models. In addition, models assume that the response of microbial respiration to moisture is the same for all ecosystems, regardless of climate history, an assumption that many empirical studies have challenged. These gaps in understanding of the microbial respiration response to moisture contribute to uncertainty in model predictions.

    We review our understanding of what drives microbial moisture response, highlighting evidence that historical precipitation can influence both responses to moisture and sensitivity to drought. We present two hypotheses, the ‘climate history hypothesis’, where we predict that baseline moisture response functions change as a function of precipitation history, and the ‘drought legacy hypothesis’, in which we suggest that the intensity and frequency of historical drought have shaped microbial communities in ways that will control moisture responses to contemporary drought. Underlying mechanisms include biological selection and filtering of the microbial community by rainfall regimes, which result in microbial traits and trade‐offs that shape function.

    Wemore »present an integrated modelling and empirical approach for understanding microbial moisture responses and improving models. Standardized measures of moisture response (respiration rate across a range of moistures) and accompanying microbial properties are needed across sites. These data can be incorporated into trait‐based models to produce generalized moisture response functions, which can then be validated and incorporated into conventional and microbially explicit ecosystem models of soil C cycling. Future studies should strive to analyse realistic moisture conditions and consider the role of environmental factors and soil structure in microbial response.

    Microbes are the engines that drive C storage and are sensitive to changes in rainfall. A greater understanding of the factors that govern this sensitivity could be a key part of improving predictions of soil C dynamics, climate change and C‐climate feedbacks.

    Read the freePlain Language Summaryfor this article on the Journal blog.

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  8. Abstract

    We use the Multiple Element Limitation (MEL) model to examine responses of 12 ecosystems to elevated carbon dioxide (CO2), warming, and 20% decreases or increases in precipitation. Ecosystems respond synergistically to elevated CO2, warming, and decreased precipitation combined because higher water‐use efficiency with elevated CO2and higher fertility with warming compensate for responses to drought. Response to elevated CO2, warming, and increased precipitation combined is additive. We analyze changes in ecosystem carbon (C) based on four nitrogen (N) and four phosphorus (P) attribution factors: (1) changes in total ecosystem N and P, (2) changes in N and P distribution between vegetation and soil, (3) changes in vegetation C:N and C:P ratios, and (4) changes in soil C:N and C:P ratios. In the combined CO2and climate change simulations, all ecosystems gain C. The contributions of these four attribution factors to changes in ecosystem C storage varies among ecosystems because of differences in the initial distributions of N and P between vegetation and soil and the openness of the ecosystem N and P cycles. The net transfer of N and P from soil to vegetation dominates the C response of forests. For tundra and grasslands, the C gain is also associated withmore »increased soil C:N and C:P. In ecosystems with symbiotic N fixation, C gains resulted from N accumulation. Because of differences in N versus P cycle openness and the distribution of organic matter between vegetation and soil, changes in the N and P attribution factors do not always parallel one another. Differences among ecosystems in C‐nutrient interactions and the amount of woody biomass interact to shape ecosystem C sequestration under simulated global change. We suggest that future studies quantify the openness of the N and P cycles and changes in the distribution of C, N, and P among ecosystem components, which currently limit understanding of nutrient effects on C sequestration and responses to elevated CO2and climate change.

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  9. Premise

    Nutrients, light, water, and temperature are key factors limiting the growth of individual plants in nature. Mutualistic interactions between plants and microbes often mediate resource limitation for both partners. In the mutualism between legumes and rhizobia, plants provide rhizobia with carbon in exchange for fixed nitrogen. Because partner quality in mutualisms is genotype‐dependent, within‐species genetic variation is expected to alter the responses of mutualists to changes in the resource environment. Here we ask whether partner quality variation in rhizobia mediates the response of host plants to changing light availability, and conversely, whether light alters the expression of partner quality variation.


    We inoculated clover hosts with 11 strains ofRhizobium leguminosarumthat differed in partner quality, grew plants under either ambient or low light conditions in the greenhouse, and measured plant growth, nodule traits, and foliar nutrient composition.


    Light availability and rhizobium inoculum interactively determined plant growth, and variation in rhizobium partner quality was more apparent in ambient light.


    Our results suggest that variation in the costs and benefits of rhizobium symbionts mediate host responses to light availability and that rhizobium strain variation might more important in higher‐light environments. Our work adds to a growing appreciation for the role of microbial intraspecific andmore »interspecific diversity in mediating extended phenotypes in their hosts and suggests an important role for light availability in the ecology and evolution of legume–rhizobium symbiosis.

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  10. Abstract

    In order to both combat the decline of biodiversity and produce food, fuel, and fiber for a growing human population, current agricultural landscapes must transition into diversified, multifunctional systems. Perennial cellulosic biofuel crops have potential to meet both of these challenges, acting as multifunctional systems that can enhance biodiversity. What is not well understood, and what we test here, are the tradeoffs among different perennial crops in their performance as biofuels and in biodiversity conservation. Working in an established bioenergy experiment with four native, perennial, cellulosic biofuel crop varieties—ranging from monoculture to diverse restoration planting—we tested the effect of biofuel crop management on flower communities, pollinator communities, and crop yield. The greatest abundance and diversity of pollinators and flowers were in treatments that were successional (unmanaged), followed by restored prairie (seeded mix of native grasses and forbs), switchgrass, and a mix of native grasses. However, biofuel crop yield was approximately the inverse, with native grasses having the highest yield, followed by switchgrass and prairie, then successional treatments. Restored prairie was the optimal biofuel crop when both pollinator conservation and crop yield are valued similarly. We add to mounting evidence that policy is needed to create sustainable markets that valuemore »the multifunctionality of perennial biofuel systems in order to achieve greater ecosystem services from agricultural landscapes.

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