Browsing by Author "Boot, Claudia M., committee member"

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Open Access
Crop domestication impacts on rhizosphere interactions and nitrogen acquisition
(Colorado State University. Libraries, 2024) Hwang, Siwook, author; Fonte, Steven J., advisor; Machmuller, Megan B., committee member; Crews, Timothy E., committee member; Wrighton, Kelly C., committee member; Boot, Claudia M., committee member
Synthetic nitrogen (N) fertilizer is an essential pillar of modern industrial agriculture. Production and application of synthetic N fertilizer, however, are two of the most expensive, energy intensive, and environmentally deleterious processes in agriculture. Therefore, alternative means of providing N in an agroecosystem are of great interest in sustainable agriculture. While many solutions – from cover cropping to intercropping – have been suggested over time it remains unclear if the modern high-yielding crops can thrive in these alternative N conditions. Decades of breeding under high synthetic N input as well as the inherently annual nature of these modern cereal crops may prevent them from fully taking advantage of these alternative N sources. In this dissertation, I explored the impact of domestication on crop rhizosphere interactions and N acquisition, in both retrospective and prospective terms. First, I investigated how modern maize (Zea mays subsp. mays), and its wild relative Teosinte (Zea mays subsp. parviglumis) differed in their ability to adapt to, and take up, cover crop residue N and synthetic N inputs. We designed a 13C (carbon)/15N dual isotope labeling experiment in which we compared the C allocation patterns of modern maize and teosinte in response to synthetic (urea) and organic (cover crop residue) forms of N. Teosinte responded to organic N by increasing its biomass root-to-shoot (R:S) ratio by 50% compared to synthetic N, while modern maize maintained the same biomass R:S ratios in both N treatments. Recent photosynthate R:S ratio (measured using 13C-CO2, 7 weeks after establishment) was greater in organic N than in synthetic N treatments for both modern maize and teosinte (91% and 37%; respectively). Label-derived dissolved organic C (DOC), representing recent rhizodeposits, was 2.5 times greater in the organic N treatments for both genotypes. Modern maize took up a similar amount of organic N as teosinte using different C allocation strategies. Our findings suggest that intensive breeding under high N input conditions has not affected this modern maize hybrid's access to organic N sources while improving its ability to take up synthetic N. Next, I shifted my focus to the novel perennial grains Kernza and perennial wheat. Kernza® is a domesticated intermediate wheatgrass (IWG, Thinopyrum intermedium). Perennial wheat is a hybrid between Kernza/IWG and modern annual durum wheat (Triticum turgidum subsp. durum). Kernza, in addition to being a perennial, may still possess beneficial belowground traits that may have been lost in modern cereals through millennia of aboveground-focused plant breeding. If so, such traits may be passed down to perennial wheat. To characterize root architecture, exudate profiles, and microbial communities of Kernza and perennial wheat in relation to annual wheat, I conducted a greenhouse experiment. We grew three genotypes/species (Kernza, perennial wheat, annual wheat) and collected their root exudates after 8 weeks of growth. The exudates were analyzed via LC-MS/MS for their chemical composition. We extracted DNA from rhizosphere soils and sequenced them for 16S and ITS profiles. Lastly, we scanned the roots to analyze root distribution across different diameter classes. We found that perennial wheat invested more heavily into very fine (< 250 µm) roots compared to annual wheat and Kernza. Perennial wheat also exuded at a greater rate of exudates per amount of root biomass. We suspect that the greater proportion of very fine roots in perennial wheat led to greater surface area and greater specific exudation rate, and that this may be related to hybrid vigor. We did not find evidence of a genotype effect on root exudate or microbial community composition. However, root exudates (overall metabolite profiles) significantly correlated with root architecture (distribution of root volume over different diameter classes) and the microbial community composition. These interactions represent a potential pathway through which plants can exert influence over the rhizosphere microbial community. Overall, these results emphasize the importance of root architecture in mediating belowground interactions. Understanding rhizosphere dynamics and the response to domestication and hybridization can guide further development of robust perennial cereal crops. In a third experiment, I studied how Kernza, perennial wheat, and annual responded to cereal-legume intercropping (biculture) in the field. To do so, we planted each of the three genotypes in monoculture or in biculture with alfalfa (Medicago sativa). We sampled their rhizosphere over two growing seasons and extracted soil DNA to construct rhizosphere 16S and ITS profiles. We hypothesized that 1) rhizosphere microbial community composition of annual wheat and Kernza will be most dissimilar from each other with perennial wheat intermediate, and 2) microbial community composition will shift in biculture, with the greatest change in Kernza and the smallest in annual wheat. We found that the rhizosphere 16S profiles differed significantly from the other two genotypes but the 16S profile of perennial wheat did not differ from that of annual wheat. Perennial wheat seemingly inherited microbial recruitment traits of its annual parent more so than its perennial parent's. Interestingly, inclusion of legumes led to the convergence, rather than divergence, of 16S profiles among genotypes. We postulate that the competitive pressure of alfalfa may have led to this convergence of 16S profiles across genotypes. The fungal community did not show evidence of genotype effect. However, the fungal community composition changed over two years in monoculture but not in biculture. This result implies that fungal community may become distinct over time if it is influenced by only one genotype (i.e., monoculture) rather than two (i.e., biculture). In conclusion, we found evidence of genotype-driven microbial community assembly that changed with legume's competitive pressure. The inheritability of microbial assembly was present but skewed towards the annual parent. Our study demonstrates the importance of including rhizosphere interactions in our evaluation of novel cereal crops in and out of cereal-legume biculture. In a final study, I investigated how rhizosphere microbial ecology of these three genotypes (Kernza, annual wheat, and perennial wheat) could be linked to their ability to acquire N from neighboring alfalfa plants. We designed a greenhouse study in which we planted all three cereals in monoculture or in biculture with alfalfa and used 15N leaf feeding technique to track the movement of N from alfalfa to cereals. In addition, we also extracted DNA from the soil and sequenced it for 16S rRNA profiles. Arbuscular mycorrhizal fungi (AMF) infection rate was also measured on all cereals and legumes. We hypothesized that: 1) annual wheat would produce the greatest biomass but Kernza would have highest proportion of legume derived N in its biomass, 2) all microbial communities will shift in biculture, with the greatest change in Kernza and the smallest in annual wheat, and 3) Kernza would have the highest rate of infection from AMF, especially in biculture. Surprisingly, we found no evidence of genotype or cropping system (monoculture or biculture) effect on either proportion or absolute amount of N derived from legume. We did find, however, that DOC concentration was higher in cereal rhizosphere grown in biculture than in monoculture, suggesting greater belowground investment in exudates when the grasses are grown with a legume. Despite this trend, annual wheat had much lower microbial biomass carbon (MBC) level in its rhizosphere compared to the perennials, in biculture. We contended that this may be due to substrate suitability of annual wheat's rhizodeposit. We also found that AMF infection rate was in fact the lowest in Kernza. Lastly, we found that 16S profiles of all three cereals shifted towards that of alfalfa in biculture. This trend might suggest microbial spillover, wherein rhizosphere microbial community of one genotype colonizes that of a neighboring plant, from alfalfa rhizosphere. Overall, we demonstrated that quantifying the N transfer in the rhizosphere can provide important insight into how these genotypes may be inducing changes in soil biogeochemistry in response to neighboring legumes. In summation, this dissertation provides links between crop genotype, root exudate chemistry and rate, microbial community assembly, and their biogeochemical consequences, in alternative N environments. Deepened understanding of how complex rhizosphere interactions may affect internal N cycling could be leveraged to further optimize these unique systems such as perennial cereal-legume biculture. In doing so, we will be one step closer to a more sustainable future, that is less reliant on synthetic N fertilizers.
Open Access
Tracing carbon flows through Arctic and alpine watersheds
(Colorado State University. Libraries, 2018) Lynch, Laurel M., author; Wallenstein, Matthew D., advisor; Boot, Claudia M., committee member; Covino, Timothy P., committee member; Cotrufo, M. Francesca, committee member
Organic matter turnover and mobilization links the productivity of terrestrial and fluvial ecosystems and regulates global climate. The first part of this dissertation reviews how our conceptual framework of soil organic matter (SOM) and dissolved organic matter (DOM) cycling has evolved, and emphasizes the role of microbial communities in controlling SOM stability. Chapter two investigates how fresh carbon (C) influences SOM cycling in soils underlying two dominant Arctic plant species. We amended soils colonized by Eriophorum vaginatum—a tussock-forming sedge—and Betula nana—a competitive dwarf shrub—with glucose, and employed stable isotope tracing to quantify substrate conversion to CO2, incorporation in microbial biomass, and retention in bulk soil. We measured responses during peak biomass, fall senescence, and spring thaw to assess interactive effects of glucose amendment and season. We also captured legacy responses to amendment by assessing the fate of glucose over short, intermediate, and longer-term periods. We found that glucose conversion to CO2 was twice as high in tussock soils, while stabilization in bulk soils was significantly higher in shrub soils. Our results highlight the extraordinary C storage capacity of these soils, and suggest shrub expansion could mitigate C losses even as Arctic soils warm. Chapter three evaluates the mobilization and transformation potential DOM of flowing through an Arctic hillslope. Widespread permafrost thaw is expected to increase CO2 release from soils to the atmosphere and transform the hydrological routing of water and DOM across Arctic landscapes. We traced the mobilization potential of DOM at two landscape positions (hillslope and riparian) and from two soil horizons (organic and mineral) using bromide, and characterized the chemical composition of DOM using solution state 1H-NMR and fluorescence spectroscopy. We found that compounds mobilized through the porous organic horizon were associated with plant-derived molecules, while those flowing through mineral soils had a microbial fingerprint. Landscape position also influenced the chemical diversity of DOM, which increased during downslope transport from hillslope to riparian soils. While the chemical composition of DOM varied across the landscape, the potential for rapid lateral flow across Arctic hillslopes and along the mineral-permafrost interface was uniformly high, suggesting DOM mobilization is an important mechanism of C loss from Arctic soils. Chapter four explores how geomorphic complexity and seasonal hydrology influence the cycling and transformation of DOM in alpine headwater streams. We collected surface and hyporheic water samples from two watersheds varying in channel complexity (single-thread and multi-thread) at eight time points spanning the seasonal hydrograph. We found that connectivity across the terrestrial-aquatic interface was maximized during peak discharge and decreased through the season. The chemical composition of DOM, evaluated using electron impact gas chromatography mass spectrometry and fluorescence spectroscopy, varied with watershed connectivity, with increasingly divergent DOM profiles observed with a loss of hydrologic connectivity. We suggest that widespread channel simplification, resulting from land-use and management changes, will reduce DOM processing and compromise ecosystem function.
Open Access
Variation in soil organic carbon across lowland tropical forest gradients: soil fertility and precipitation effects on soil carbon organic chemistry and age
(Colorado State University. Libraries, 2022) Blackaby, Emily, author; Cusack, Daniela F., advisor; Boot, Claudia M., committee member; Cotrufo, M. Francesca, committee member
Tropical forests hold large amounts of carbon (C) in both aboveground biomass and belowground soil organic carbon (SOC) stocks. Climate change is expected to alter tropical forests' precipitation with some forests already showing decreased rainfall. We analyzed SOC molecular composition and age in lowland tropical forests of Panama across fertility gradients, rainfall ranges, and soil order. We hypothesized that H1) rainforests with relatively greater rainfall store larger amounts of proteins (N-alkyl) and lipids (alkyl) in SOC because of greater microbial biomass and H2) subsurface SOC stocks in more strongly weathered, clay-rich soils are older (as indicated by radiocarbon) because of great sorption capacity. We found that overall, carbon decreased and became older with depth across all samples. Solid-state 13C NMR spectroscopy indicated that soil order and depth were significant predictors of C functional group abundances while phosphorus (P) was a significant predictor of alkyl, aromatic, and carboxyl C. Alkyl/O-Alkyl ratios increased with depth indicating increased degradation of the SOC. ∆14C values indicated older C with depth and varied significantly with soil order where Oxisols were the oldest and Mollisols the youngest. Soil N % and K % were significant predictors of younger soil C. Additionally, biomolecular composition of SOM from 0-10 cm was a significant predictor of ∆14C at 25-50 cm. We found that higher abundances of alkyl and O-alkyl C corresponded with younger C at depth and higher abundances of aromatic and phenolic C contained older C at depth.