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1. Nitrogen Fixation and Resorption Efficiency Differences Among Twelve Upland and Lowland Switchgrass Cultivars

   https://doi.org/10.1094/PBIOMES-11-19-0064-FI  

   Roley, Sarah S. ; Ulbrich, Tayler C. ; Robertson, G. Philip ( January 2021 , Phytobiomes Journal)

   null (Ed.)

   In nitrogen (N)-limited terrestrial ecosystems, plants employ various strategies to acquire and conserve N, including translocation of N in perennial tissues and stimulation of N fixation in roots and soils. Switchgrass (Panicum virgatum) is a genotypically and phenotypically diverse perennial grass with two distinct ecotypes (lowland and upland) and numerous genotypes. It grows well in low-N soils, likely because of its ability to translocate N and to associate with N-fixing microbes, but little is known about variation in these traits among cultivars or even ecotypes. We measured N translocation, N fixation potential in roots and soils, soil net N mineralization, soil net nitrification, and biomass yields in 12 switchgrass cultivars grown in a replicated block experiment in southwestern Michigan, United States. Lowland cultivars had higher yields, rates of N translocation, soil net N mineralization, and N fixation potentials on washed, nonsterile roots, while upland cultivars exhibited higher N fixation potentials in root-free soil. N resorption efficiencies averaged 53 ± 5% (± standard error) for lowland versus 29 ± 3% for upland cultivars. Additionally, there were significant among-cultivar differences for all response variables except mineralization and nitrification, with differences likely explained by cultivar-specific physiologies and microbial communities. The ideal cultivar for biofuels is one that can maintain high yields with minimal fertilizer addition, and there appear to be several cultivars that meet these criteria. In addition, results suggest substantial N cycle differences among cultivars that might be exploited by breeders to create new or improved high-yielding, N-conserving switchgrass lines. 

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2. Switchgrass (Panicum virgatum L.) cultivars have similar impacts on soil carbon and nitrogen stocks and microbial function

   https://doi.org/10.1111/gcbb.13125  

   Mosier, Samantha ; Kelly, Lauren ; Ozlu, Ekrem ; Robertson, G. Philip ( March 2024 , GCB Bioenergy)

   Switchgrass (Panicum virgatum L.) production for biofuel has the potential to produce reasonable yields on lands not suited for conventional agriculture. We assessed nine switchgrass cultivars representing lowland and upland ecotypes grown for 11 years at a site in the upper Midwest USA for belowground differences in soil carbon and nitrogen stocks, soil organic matter fractions, and standing root biomass to 1 m depth. We also compared potential nitrogen mineralization and carbon substrate use through community‐level physiological profiling in surface soils (0–10 cm depth). Average yields and standing root biomass differed among cultivars and between ecotypes, but we found no significant cultivar‐related impacts on soil carbon and nitrogen stocks, on the distribution of particulate and mineral‐associated soil organic matter fractions, nor on potential nitrogen mineralization or microbial community‐level physiological profiles. That these traits did not differ among cultivars suggests that soil carbon and nitrogen gains under switchgrass are likely to be robust with respect to cultivar differences, and to this point not much affected by breeding efforts. 

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3. Regional biogeography versus intra-annual dynamics of the root and soil microbiome

   https://doi.org/10.1186/s40793-023-00504-x  

   Bell-Dereske, Lukas P. ; Benucci, Gian Maria Niccolò ; da Costa, Pedro Beschoren ; Bonito, Gregory ; Friesen, Maren L. ; Tiemann, Lisa K. ; Evans, Sarah E. ( June 2023 , Environmental Microbiome)

   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, 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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4. Home-field advantage affects the local adaptive interaction between Andropogon gerardii ecotypes and root-associated bacterial communities

   https://doi.org/10.1128/spectrum.00208-23  

   Kazarina, Anna ; Sarkar, Soumyadev ; Thapa, Shiva ; Heeren, Leah ; Kamke, Abgail ; Ward, Kaitlyn ; Hartung, Eli ; Ran, Qinghong ; Galliart, Matthew ; Jumpponen, Ari ; et al ( October 2023 , Microbiology Spectrum)

   Arias, Renee S. (Ed.)

   Due to climate change, drought frequencies and severities are predicted to increase across the United States. Plant responses and adaptation to stresses depend on plant genetic and environmental factors. Understanding the effect of those factors on plant performance is required to predict species’ responses to environmental change. We used reciprocal gardens planted with distinct regional ecotypes of the perennial grassAndropogon gerardiiadapted to dry, mesic, and wet environments to characterize their rhizosphere communities using 16S rRNA metabarcode sequencing. Even though the local microbial pool was the main driver of these rhizosphere communities, the significant plant ecotypic effect highlighted active microbial recruitment in the rhizosphere, driven by ecotype or plant genetic background. Our data also suggest that ecotypes planted at their homesites were more successful in recruiting rhizosphere community members that were unique to the location. The link between the plants’ homesite and the specific local microbes supported the “home field advantage” hypothesis. The unique homesite microbes may represent microbial specialists that are linked to plant stress responses. Furthermore, our data support ecotypic variation in the recruitment of congeneric but distinct bacterial variants, highlighting the nuanced plant ecotype effects on rhizosphere microbiome recruitment. These results improve our understanding of the complex plant host–soil microbe interactions and should facilitate further studies focused on exploring the functional potential of recruited microbes. Our study has the potential to aid in predicting grassland ecosystem responses to climate change and impact restoration management practices to promote grassland sustainability.

   In this study, we used reciprocal gardens located across a steep precipitation gradient to characterize rhizosphere communities of distinct dry, mesic, and wet regional ecotypes of the perennial grassAndropogon gerardii. We used 16S rRNA amplicon sequencing and focused oligotyping analysis and showed that even though location was the main driver of the microbial communities, ecotypes could potentially recruit distinct bacterial populations. We showed that differentA. gerardiiecotypes were more successful in overall community recruitment and recruitment of microbes unique to the “home” environment, when growing at their “home site.” We found evidence for “home-field advantage” interactions between the host and host–root-associated bacterial communities, and the capability of ecotypes to recruit specialized microbes that were potentially linked to plant stress responses. Our study aids in a better understanding of the factors that affect plant adaptation, improve management strategies, and predict grassland function under the changing climate.

    

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5. Terpenes modulate bacterial and fungal growth and sorghum rhizobiome communities

   https://doi.org/10.1128/spectrum.01332-23  

   Chou, Ming-Yi ; Andersen, Trine B. ; Mechan Llontop, Marco E. ; Beculheimer, Nick ; Sow, Alassane ; Moreno, Nick ; Shade, Ashley ; Hamberger, Bjoern ; Bonito, Gregory ; Calatrava, Victoria ( October 2023 , Microbiology Spectrum)

   Hom, Erik F. (Ed.)

   Terpenes are among the oldest and largest class of plant-specialized bioproducts that are known to affect plant development, adaptation, and biological interactions. While their biosynthesis, evolution, and function in aboveground interactions with insects and individual microbial species are well studied, how different terpenes impact plant microbiomes belowground is much less understood. Here we designed an experiment to assess how belowground exogenous applications of monoterpenes (1,8-cineole and linalool) and a sesquiterpene (nerolidol) delivered through an artificial root system impacted its belowground bacterial and fungal microbiome. We found that the terpene applications had significant and variable impacts on bacterial and fungal communities, depending on terpene class and concentration; however, these impacts were localized to the artificial root system and the fungal rhizosphere. We complemented this experiment with pure culture bioassays on responsive bacteria and fungi isolated from the sorghum rhizobiome. Overall, higher concentrations (200 µM) of nerolidol were inhibitory toFerrovibriumand tested Firmicutes. While fungal isolates ofPenicilliumandPericoniawere also more inhibited by higher concentrations (200 µM) of nerolidol,Clonostachyswas enhanced at this higher level and together withHumicolawas inhibited by the lower concentration tested (100 µM). On the other hand, 1,8-cineole had an inhibitory effect onOrbiliaat both tested concentrations but had a promotive effect at 100 µM onPenicilliumandPericonia. Similarly, linalool at 100 µM had significant growth promotion inMortierella, but an inhibitory effect forOrbilia. Together, these results highlight the variable direct effects of terpenes on single microbial isolates and demonstrate the complexity of microbe-terpene interactions in the rhizobiome.

   Terpenes represent one of the largest and oldest classes of plant-specialized metabolism, but their role in the belowground microbiome is poorly understood. Here, we used a “rhizobox” mesocosm experimental set-up to supply different concentrations and classes of terpenes into the soil compartment with growing sorghum for 1 month to assess how these terpenes affect sorghum bacterial and fungal rhizobiome communities. Changes in bacterial and fungal communities between treatments belowground were characterized, followed by bioassays screening on bacterial and fungal isolates from the sorghum rhizosphere against terpenes to validate direct microbial responses. We found that microbial growth stimulatory and inhibitory effects were localized, terpene specific, dose dependent, and transient in time. This work paves the way for engineering terpene metabolisms in plant microbiomes for improved sustainable agriculture and bioenergy crop production.

    

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