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1. Electrochemically Active Biofilms as an Indicator of Soil Health

   https://doi.org/10.1149/1945-7111/ac1e56  

   Mohamed, Abdelrhman; Sanchez, Eduardo; Sanchez, Natalie; Friesen, Maren L.; Beyenal, Haluk (August 2021, Journal of The Electrochemical Society)

   Soil health is a complex phenomenon that reflects the ability of soil to support both plant growth and other ecosystem functions. To our knowledge, research on extracellular electron transfer processes in soil environments is limited and could provide novel knowledge and new ways of monitoring soil health. Electrochemical activities in the soil can be studied by inserting inert electrodes. Once the electrode is polarized to a favorable potential, nearby microorganisms attach to the electrodes and grow as biofilms. Biofilms are a major part of the soil and play critical roles in microbial activity and community dynamics. Our work aims to investigate the electrochemical behavior of healthy and unhealthy soils using chronoamperometry and cyclic voltammetry. We developed a bioelectrochemical soil reactor for electrochemical measurements using healthy and unhealthy soils taken from the Cook Agronomy Farm Long-Term Agroecological Research site; the soils showed similar physical and chemical characteristics, but there was higher plant growth where the healthy soil was taken. Using carbon cloth electrodes installed in these soil reactors, we explored the electrochemical signals in these two soils. First, we measured redox variations by depth and found that reducing conditions were prevalent in healthy soils. Current measurements showed distinct differences between healthy and unhealthy soils. Scanning electron microscopy images showed the presence of microbes attached to the electrode for healthy soil but not for unhealthy soil. Glucose addition stimulated current in both soil types and caused differences in cyclic voltammograms between the two soil types to converge. Our work demonstrates that we can use current as a proxy for microbial metabolic activity to distinguish healthy and unhealthy soil. 

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2. Distinct microbial communities alter litter decomposition rates in a fertilized coastal plain wetland

   https://doi.org/10.1002/ecs2.3619  

   Koceja, Megan_E; Bledsoe, Regina_B; Goodwillie, Carol; Peralta, Ariane_L (June 2021, Ecosphere)

   Abstract Human activities have led to increased deposition of nitrogen (N) and phosphorus (P) into soils. Nutrient enrichment of soils is known to increase plant biomass and rates of microbial litter decomposition. However, interacting effects of hydrologic position and associated changes to soil moisture can constrain microbial activity and lead to unexpected nutrient feedbacks on microbial community structure–function relationships. Examining feedbacks of nutrient enrichment on decomposition rates is essential for predicting microbial contributions to carbon (C) cycling as atmospheric deposition of nutrients persists. This study explored how long‐term nutrient addition and contrasting litter chemical composition influenced soil bacterial community structure and function. We hypothesized that long‐term nutrient enrichment of low fertility soils alters bacterial community structure and leads to higher rates of litter decomposition especially for low C:N litter, but low‐nutrient and dry conditions limit microbial decomposition of high C:N ratio litter. We leveraged a long‐term fertilization experiment to test how nutrient enrichment and hydrologic manipulation (due to ditches) affected decomposition and soil bacterial community structure in a nutrient‐poor coastal plain wetland. We conducted a litter bag experiment and characterized litter‐associated and bulk soil microbiomes using 16S rRNA bacterial sequencing and quantified litter mass losses and soil physicochemical properties. Results revealed that distinct bacterial communities were involved in decomposing higher C:N ratio litter more quickly in fertilized compared to unfertilized soils especially under drier soil conditions, while decomposition rates of lower C:N ratio litter were similar between fertilized and unfertilized plots. Bacterial community structure in part explained litter decomposition rates, and long‐term fertilization and drier hydrologic status affected bacterial diversity and increased decomposition rates. However, community composition associated with high C:N litter was similar in wetter plots with available nitrate detected, regardless of fertilization treatment. This study provides insight into long‐term fertilization effects on soil bacterial diversity and composition, decomposition, and the increased potential for soil C loss as nutrient enrichment and hydrology interact to affect historically low‐nutrient ecosystems. 

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3. Nonlinear responses of ericaceous and ectomycorrhizal Arctic shrubs across a long‐term experimental nutrient gradient

   https://doi.org/10.1002/ecs2.4888  

   Dunleavy, Haley R; Mack, Michelle C (July 2024, Ecosphere)

   Abstract In the Arctic tundra, warming is anticipated to stimulate nutrient release and potentially alleviate plant nutrient limitations. Typically simulated by fertilization experiments that saturate plant nutrient demand, future increases in soil fertility are thought to favor ectomycorrhizal (EcM) over ericaceous shrubs and have often been identified as a key driver of Arctic shrub expansion. However, the projected increases in fertility will likely vary in their alleviation of nutrient limitations. The resulting responses of shrubs and their mycorrhizae across the gradient of nutrient limitation may be nonlinear and could contradict the current predictions of tundra vegetation shifts. We compared the functional responses of two dominant shrubs, EcM dwarf birch (Betula nana) and ericaceous Labrador tea (Rhododendron tomentosum), across a long‐term nitrogen and phosphorus fertilization gradient experiment in Arctic Alaska. Using linear mixed‐effects modeling, we tested the responses of shrub cover, height, and root enzyme activities to soil fertility. We found thatB. nanacover and height linearly increased with soil fertility. In contrast,R. tomentosumcover initially increased, but decreased after surpassing the intermediate levels of increased soil fertility. Its height did not change. Enzyme activity did not respond to soil fertility on EcM‐colonizedB. nanaroots, but sharply declined onR. tomentosumroots. Overall, the nonlinear responses of shrubs to our fertility gradient demonstrate the importance of experiments grounded in replicated regression design. Our results indicate that under moderate increases in soil fertility, Arctic shrub expansion may not only include deciduous EcM shrubs but also ericaceous shrubs. Regardless of shifts aboveground, changes in root enzyme activity belowground point to some EcM shrub species playing a more influential role in tundra soils; as EcM roots remained steady in their liberation of soil organic nutrients with heightened soil fertility, degradative root enzyme activity on the dominant ericaceous shrub dropped—in some instances with even the slightest increase in fertility. 

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4. Long-Term Nutrient Enrichment of an Oligotroph-Dominated Wetland Increases Bacterial Diversity in Bulk Soils and Plant Rhizospheres

   https://doi.org/10.1128/mSphere.00035-20  

   Bledsoe, Regina B.; Goodwillie, Carol; Peralta, Ariane L. (June 2020, mSphere)

   Campbell, Barbara J. (Ed.)

   ABSTRACT In nutrient-limited conditions, plants rely on rhizosphere microbial members to facilitate nutrient acquisition, and in return, plants provide carbon resources to these root-associated microorganisms. However, atmospheric nutrient deposition can affect plant-microbe relationships by changing soil bacterial composition and by reducing cooperation between microbial taxa and plants. To examine how long-term nutrient addition shapes rhizosphere community composition, we compared traits associated with bacterial (fast-growing copiotrophs, slow-growing oligotrophs) and plant (C 3 forb, C 4 grass) communities residing in a nutrient-poor wetland ecosystem. Results revealed that oligotrophic taxa dominated soil bacterial communities and that fertilization increased the presence of oligotrophs in bulk and rhizosphere communities. Additionally, bacterial species diversity was greatest in fertilized soils, particularly in bulk soils. Nutrient enrichment (fertilized versus unfertilized) and plant association (bulk versus rhizosphere) determined bacterial community composition; bacterial community structure associated with plant functional group (grass versus forb) was similar within treatments but differed between fertilization treatments. The core forb microbiome consisted of 602 unique taxa, and the core grass microbiome consisted of 372 unique taxa. Forb rhizospheres were enriched in potentially disease-suppressive bacterial taxa, and grass rhizospheres were enriched in bacterial taxa associated with complex carbon decomposition. Results from this study demonstrate that fertilization serves as a strong environmental filter on the soil microbiome, which leads to distinct rhizosphere communities and can shift plant effects on the rhizosphere microbiome. These taxonomic shifts within plant rhizospheres could have implications for plant health and ecosystem functions associated with carbon and nitrogen cycling. IMPORTANCE Over the last century, humans have substantially altered nitrogen and phosphorus cycling. Use of synthetic fertilizer and burning of fossil fuels and biomass have increased nitrogen and phosphorus deposition, which results in unintended fertilization of historically low-nutrient ecosystems. With increased nutrient availability, plant biodiversity is expected to decline, and the abundance of copiotrophic taxa is anticipated to increase in bacterial communities. Here, we address how bacterial communities associated with different plant functional types (forb, grass) shift due to long-term nutrient enrichment. Unlike other studies, results revealed an increase in bacterial diversity, particularly of oligotrophic bacteria in fertilized plots. We observed that nutrient addition strongly determines forb and grass rhizosphere composition, which could indicate different metabolic preferences in the bacterial communities. This study highlights how long-term fertilization of oligotroph-dominated wetlands could alter diversity and metabolism of rhizosphere bacterial communities in unexpected ways. 

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5. Shifts in bacterial traits under chronic nitrogen deposition align with soil processes in arbuscular, but not ectomycorrhizal‐associated trees

   https://doi.org/10.1111/gcb.17030  

   Piñeiro, Juan; Dang, Chansotheary; Walkup, Jeth_G_V; Kuzniar, Teagan; Winslett, Rachel; Blazewicz, Steven_J; Freedman, Zachary_B; Brzostek, Edward; Morrissey, Ember_M (November 2023, Global Change Biology)

   Abstract Nitrogen (N) deposition increases soil carbon (C) storage by reducing microbial activity. These effects vary in soil beneath trees that associate with arbuscular (AM) and ectomycorrhizal (ECM) fungi. Variation in carbon C and N uptake traits among microbes may explain differences in soil nutrient cycling between mycorrhizal associations in response to high N loads, a mechanism not previously examined due to methodological limitations. Here, we used quantitative Stable Isotope Probing (qSIP) to measure bacterial C and N assimilation rates from an added organic compound, which we conceptualize as functional traits. As such, we applied a trait‐based approach to explore whether variation in assimilation rates of bacterial taxa can inform shifts in soil function under chronic N deposition. We show taxon‐specific and community‐wide declines of bacterial C and N uptake under chronic N deposition in both AM and ECM soils. N deposition‐induced reductions in microbial activity were mirrored by declines in soil organic matter mineralization rates in AM but not ECM soils. Our findings suggest C and N uptake traits of bacterial communities can predict C cycling feedbacks to N deposition in AM soils, but additional data, for instance on the traits of fungi, may be needed to connect microbial traits with soil C and N cycling in ECM systems. Our study also highlights the potential of employing qSIP in conjunction with trait‐based analytical approaches to inform how ecological processes of microbial communities influence soil functioning. 

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