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1. High interspecific variation in nutrient excretion within a guild of closely related caddisfly species

   https://doi.org/10.1002/ecs2.2205  

   Balik, J.A.; Taylor, B.W.; Washko, S.E.; Wissinger, S.A. (May 2018, Ecosphere)

   Understanding the amount of variation in functional traits between closely related species within guilds is critical for understanding links between community composition and ecosystem processes. Nutrient excretion is an important link between animals and their environments, and aquatic invertebrate communities can supply a considerable proportion of ecosystem nutrient demand via excretion. We quantified nitrogen (N) and phosphorus (P) excretion rates of 10 species of larval caddis- flies that inhabit high-elevation ponds and wetlands to determine the magnitude of variation in nutrient excretion within this guild. We found considerable interspecific variation in biomass-specific excretion of nitrogen (eightfold differences), phosphorus (sevenfold differences), and the stoichiometric N:P ratios (fivefold differences). Through a meta-analysis, we compared the variation within this guild to the variation found in other family-level species assemblages to determine the overall range in the variation of nutrient excretion that could be expected across guilds and to determine whether the variation in this caddisfly guild is comparatively extreme, average, or low. The meta-analysis revealed a large range in variation among guilds, and comparatively, the variation within this caddisfly guild is high for N excretion and intermediate for P excretion. The considerable variation within guilds revealed by our metaanalysis suggests that functional redundancy among guild members is difficult to predict. Thus, some natural or human-caused species gains or losses within biological groupings such as guilds and trophic levels could have little or no effect on ecosystem processes, whereas others could have very large effects 

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2. Inferring resource competition in microbial communities from time series

   https://doi.org/10.1101/2025.01.08.631910  

   Chen, Xiaowen; Crocker, Kyle; Kuehn, Seppe; Walczak, Aleksandra M; Mora, Thierry (January 2025, bioRxiv)

   The competition for resources is a defining feature of microbial communities. In many contexts, from soils to host-associated communities, highly diverse microbes are organized into metabolic groups or guilds with similar resource preferences. The resource preferences of individual taxa that give rise to these guilds are critical for understanding fluxes of resources through the community and the structure of diversity in the system. However, inferring the metabolic capabilities of individual taxa, and their competition with other taxa, within a community is challenging and unresolved. Here we address this gap in knowledge by leveraging dynamic measurements of abundances in communities. We show that simple correlations are often misleading in predicting resource competition. We show that spectral methods such as the cross-power spectral density (CPSD) and coherence that account for time-delayed effects are superior metrics for inferring the structure of resource competition in communities. We first demonstrate this fact on synthetic data generated from consumer-resource models with time-dependent resource availability, where taxa are organized into groups or guilds with similar resource preferences. By applying spectral methods to oceanic plankton time-series data, we demonstrate that these methods detect interaction structures among species with similar genomic sequences. Our results indicate that analyzing temporal data across multiple timescales can reveal the underlying structure of resource competition within communities. 

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3. Functional regimes define the response of the soil microbiome to environmental change

   https://doi.org/10.1101/2024.03.15.584851  

   Lee, Kiseok Keith; Liu, Siqi; Crocker, Kyle; Huggins, David R; Tikhonov, Mikhail; Mani, Madhav; Kuehn, Seppe (March 2024, bioRxiv)

   Abstract The metabolic activity of soil microbiomes plays a central role in carbon and nitrogen cycling. Given the changing climate, it is important to understand how the metabolism of natural communities responds to environmental change. However, the ecological, spatial, and chemical complexity of soils makes understanding the mechanisms governing the response of these communities to perturbations challenging. Here, we overcome this complexity by using dynamic measurements of metabolism in microcosms and modeling to reveal regimes where a few key mechanisms govern the response of soils to environmental change. We sample soils along a natural pH gradient, construct >1500 microcosms to perturb the pH, and quantify the dynamics of respiratory nitrate utilization, a key process in the nitrogen cycle. Despite the complexity of the soil microbiome, a minimal mathematical model with two variables, the quantity of active biomass in the community and the availability of a growth-limiting nutrient, quantifies observed nitrate utilization dynamics across soils and pH perturbations. Across environmental perturbations, changes in these two variables give rise to three functional regimes each with qualitatively distinct dynamics of nitrate utilization over time: a regime where acidic perturbations induce cell death that limits metabolic activity, a nutrientlimiting regime where nitrate uptake is performed by dominant taxa that utilize nutrients released from the soil matrix, and a resurgent growth regime in basic conditions, where excess nutrients enable growth of initially rare taxa. The underlying mechanism of each regime is predicted by our interpretable model and tested via amendment experiments, nutrient measurements, and sequencing. Further, our data suggest that the long-term history of environmental variation in the wild influences the transitions between functional regimes. Therefore, quantitative measurements and a mathematical model reveal the existence of qualitative regimes that capture the mechanisms and dynamics of a community responding to environmental change. 

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4. Temporally Selective Modification of the Tomato Rhizosphere and Root Microbiome by Volcanic Ash Fertilizer Containing Micronutrients

   https://doi.org/10.1128/aem.00049-22  

   Mehlferber, Elijah C.; McCue, Kent F.; Ferrel, Jon E.; Koskella, Britt; Khanna, Rajnish (April 2022, Applied and Environmental Microbiology)

   Semrau, Jeremy D. (Ed.)

   ABSTRACT Food crops are grown with fertilizers containing nitrogen, phosphorus, and potassium (macronutrients) along with magnesium, calcium, boron, and zinc (micronutrients) at different ratios during their cultivation. Soil and plant-associated microbes have been implicated to promote plant growth, stress tolerance, and productivity. However, the high degree of variability across agricultural environments makes it difficult to assess the possible influences of nutrient fertilizers on these microbial communities. Uncovering the underlying mechanisms could lead us to achieve consistently improved food quality and productivity with minimal environmental impacts. For this purpose, we tested a commercially available fertilizer (surface-mined volcanic ash deposit Azomite) applied as a supplement to the normal fertilizer program of greenhouse-grown tomato plants. Because this treatment showed a significant increase in fruit production at measured intervals, we examined its impact on the composition of below-ground microbial communities, focusing on members identified as “core taxa” that were enriched in the rhizosphere and root endosphere compared to bulk soil and appeared above their predicted neutral distribution levels in control and treated samples. This analysis revealed that Azomite had little effect on microbial composition overall, but it had a significant, temporally selective influence on the core taxa. Changes in the composition of the core taxa were correlated with computationally inferred changes in functional pathway enrichment associated with carbohydrate metabolism, suggesting a shift in available microbial nutrients within the roots. This finding exemplifies how the nutrient environment can specifically alter the functional capacity of root-associated bacterial taxa, with the potential to improve crop productivity. IMPORTANCE Various types of soil fertilizers are used routinely to increase crop yields globally. The effects of these treatments are assessed mainly by the benefits they provide in increased crop productivity. There exists a gap in our understanding of how soil fertilizers act on the plant-associated microbial communities. The underlying mechanisms of nutrient uptake are widely complex and, thus, difficult to evaluate fully but have critical influences on both soil and plant health. Here, we presented a systematic approach to analyzing the effects of fertilizer on core microbial communities in soil and plants, leading to predictable outcomes that can be empirically tested and used to develop simple and affordable field tests. The methods described here can be used for any fertilizer and crop system. Continued effort in advancing our understanding of how fertilizers affect plant and microbe relations is needed to advance scientific understanding and help growers make better-informed decisions. 

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5. 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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