Doctor of Philosophy / Department of Agronomy / Charles W. Rice / Gretchen F. Sassenrath / Soil microorganisms are a critical component of ecosystem services provided by soil. Soil management drives soil physical, chemical, and biological properties. Pedogenesis and management interact to change microbial structure and function in the soil profile. Soil microbial properties may vary temporally with crop development and crop species. The objective of this study was to explore the pedogenetic and anthropogenic controls on key soil microbial properties by (i) assessing the profile of a claypan soil under conventional tillage (CT), no-till (NT), and hay meadow (HM); (ii) assessing seasonal changes of soil microbial properties in a corn/winter wheat/soybean rotation under CT and NT; and (iii) assessing vertical changes of soil microbial properties in response to long-term (28 yrs) tillage and mineral and organic fertilization. Selected microbial properties included extracellular enzyme activity, microbial structure as measured by phospholipid fatty acid (PLFA), as well as soil chemical properties. Soil C, enzyme activities, and microbial biomass were greatest in HM soils, followed by NT and then CT in the claypan soil. Wheat in the rotation increased hydrolase activity and bacterial biomass more than corn, while microbial activities were stable during soybean growth. Increased enzyme activities in the claypan layer resulted from the combination of clay-enzyme interaction and impacts from management practices. In a Mollisol soil, an increase in C-acquiring enzyme activity and microbial PLFAs in a buried A horizon was a result of root growth under no-till practice and mineral fertilization. Surprisingly, long-term mineral fertilizer applications had little effect on enzyme activities and microbial biomass. Long-term organic fertilization increased soil C, enzyme activities, and PLFAs but decreased arbuscular mycorrhizal fungi (AMF) throughout the soil profile to a depth of 90 cm. Microbial properties are controlled by crop and soil management at the soil surface and by the interaction of management and pedogenetic properties deeper in the soil profile. Incorporating grasses in the crop rotation may allow nutrients to be extracted from deeper within the soil profile, enhancing the utilization of the entire soil profile and providing additional nutrient resources to cash crops. Incorporating wheat in the crop rotation supports greater microbial activity and biomass after corn harvest, especially in no-till management. Additional research is required to delineate further causative factors impacting enzyme activity in the claypan layer, a finer resolution in soil microbial community at the species level to explore the linkage between ecological function and microbiome structure, and a network analysis for the soil-plant-microbe interactions.

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<p>Investigating the presence of microbial communities in the Earth's deep terrestrial subsurface and the metabolic processes taking place in these environments provides insight into the some of the ultimate limits for life on Earth, as well as the potential for microbial life to exist within the subsurface of other planetary bodies. This Master's thesis project utilized phospholipid fatty acid (PLFA) analysis, in combination with carbon isotope analyses (δ¹³C and Δ¹⁴C), to explore the presence and activity of microbial communities living within deep terrestrial subsurface fracture water systems and low permeability, deep sedimentary rocks. Deep fracture water systems, ranging from 0.9 to 3.2 km below land surface, were sampled for microbial communities via deep mine boreholes in the Witwatersrand Basin of South Africa. PLFA concentrations revealed low biomass microbial communities, ranging from 2x10¹ to 5x10⁴ cells per mL and the PLFA profiles contained indicators for environmental stressors, including high temperatures and nutrient deprivation. δ¹³C and Δ¹⁴C analyses of PLFAs and potential carbon sources (dissolved inorganic carbon (DIC), dissolved organic carbon (DOC) and methane) identified microbial utilization of methane in some systems and utilization of DIC in others. Evidence for microbial oxidation of methane and chemoautotrophy in these systems is consistent with a self-sustaining deep terrestrial subsurface biosphere that is capable of surviving independent of the photosphere. Viable microbial communities were also identified within deep (334 to 694 m depth) sedimentary rock cores sampled from the Michigan Basin, Canada. PLFA analyses revealed microbial cell densities ranging from 1-3 x 10⁵ cells/mL and identified PLFA indicators for environmental stressors. These results demonstrate the ubiquity of microbial life in the deep terrestrial subsurface and provide insight into microbial carbon sources and cycling in deep microbial systems which may persist in isolation over geologic timescales.</p> / Master of Science (MSc)

Recent work has demonstrated that vast amounts of soil organic carbon (SOC) are redistributed and buried within Canadian croplands; however, the effects of redistribution on SOC dynamics and biological properties of the soil environment remain unknown. Because soil microorganisms are drivers of carbon (C) turnover in soil, the effects of such processes on microbial community dynamics are important in assessing the overall effects of redistribution and the stability of displaced C. This is particularly important in the face of future climate change scenarios and potential disturbances. The objectives of this study were to examine microbial community dynamics with depth and among landscape positions in an eroded landscape, and to assess C mineralization response between surface and subsurface soil layers in a depositional position. Microbial abundance was highly influenced by SOC redistribution. This was most evident in the buried backslope position where substantial soil and SOC deposition had occurred, creating a very thick A horizon (ca. 80 cm). Phospholipid fatty acid (PLFA) analysis revealed substantial concentrations of microbial biomass located at depth (30-60 cm), which was greater than PLFA concentration at the soil surface and correlated with SOC concentration. Community structure analysis demonstrated the strong influence of landscape position and depth in structuring microbial communities near the soil surface (0-20 cm). Communities in positions that were predominantly erosional were the most different from those in the depositional position, accounting for the largest amount of variation (60%) in the overall analysis. The existence of distinct microbial communities found in depositional material (0-25 cm) and within the buried A horizon (30-80 cm) in the buried backslope position indicate a strong influence of depth and redistribution in structuring microbial communities. The existence of significant viable biomass in the buried A horizon of the depositional position leads to question the persistence of highly concentrated, buried SOC over many decades. When soils from surface (0-5 and 20-25 cm) and subsurface (40-45 and 65-70 cm) depths were incubated in surface-like conditions, greater mineralization response in surface relative to subsurface soils, despite relatively similar SOC concentration, suggests that redistribution protects buried C from decomposition. Distinct microbial communities found at the onset and completion of the mineralization study between surface and subsurface soil layers may indicate the influence of microbial community structure on mineralization response. Depth was the largest source of variation in microbial community structure, and although a shift occurred after exposure to incubation conditions, the effect of depth remained the strongest influence. This work indicates that SOC redistribution strongly influences microbial abundance and community structure development, primarily driven by altered substrate gradients occurring with depth, and suggests that C is less susceptible to decomposition once buried in depositional positions.

Climate change is likely to alter plant species composition and interactions between plants and soil microbes that together dictate the quantity and quality of forage produced in pastures, the base of animal production in central Kentucky. This study assessed the seasonal dynamics of soil microbes and their response to increased temperature (+3oC) and growing season precipitation (+30% of the mean annual). Total soil microbial biomass, community composition, enzyme activities, potential carbon mineralization, and catabolic responses to selected substrates were measured seasonally in the different climate treatments. In this system, seasonal variability was a dominant driving factor for all the soil microbial characteristics that I investigated. Summer maxima and winter minima were identified in the active microbial biomass, while soil microbial community structure differed between each season. Extracellular enzyme activities were generally highest in either the spring or summer, while seasonal patterns for each substrate were unique across catabolic response profiles. Climate treatments produced few significant main or interactive effects on the soil microbial biomass and function. This resiliency, coupled with evidence of functional redundancy, suggests that central Kentucky pasture ecosystems may be well-equipped to handle future environmental stress associated with climate change and to maintain critical ecosystem services.

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Pulses are an important component in crop rotations in the semiarid Brown soil zone of southern Saskatchewan, Canada. Besides their capability to fix nitrogen, pulse crops establish a strong symbiotic relationship with arbuscular mycorrhizal fungi (AMF), which have been shown to increase nutrient and water uptake through hyphal extensions in the soil. Incorporating strongly mycorrhizal crops in a rotation may increase inoculum levels in the soil and benefit the growth of a subsequent crop. The objective of this study was to determine if AMF potential and colonization of a durum crop is significantly affected by cropping history and to assess the impact of pulses in crop rotations on the abundance and diversity of AMF communities in the soil. In 2004 and 2005, soil, plant, and root samples were taken on Triticum turgidum L. (durum) with preceding crops of Pisum sativum L. (pea), Lens culinaris Medik (lentil), Cicer arietinum L. (chickpea), Brassica napus L. (canola) or Triticum turgidum L. (durum). Although there were few differences in soil N and P levels, previous crop had a significant effect (p<0.05) on durum yields in both years. A previous crop of pea was associated with the highest yields, while the durum monocultures were lowest. Arbuscular mycorrhizal potential and colonization were significantly affected (p<0.05) by cropping history, but not consistently as a result of inclusion of a pulse crop. Phospholipid and neutralipid fatty acids (PLFA/NLFA) were completed to analyse the relative abundance of AMF (C16:1ù5), saprophytic fungi (C18:2ù6), and bacteria in the soil. The effect of treatment on the abundance of AMF, saprotrophic fungi and bacteria were not significant (p<0.05), but the changes over time were. These results demonstrate that although previous crop may play a role in microbial community structure, it is not the only influencing factor.

Pulses are an important component in crop rotations in the semiarid Brown soil zone of southern Saskatchewan, Canada. Besides their capability to fix nitrogen, pulse crops establish a strong symbiotic relationship with arbuscular mycorrhizal fungi (AMF), which have been shown to increase nutrient and water uptake through hyphal extensions in the soil. Incorporating strongly mycorrhizal crops in a rotation may increase inoculum levels in the soil and benefit the growth of a subsequent crop. The objective of this study was to determine if AMF potential and colonization of a durum crop is significantly affected by cropping history and to assess the impact of pulses in crop rotations on the abundance and diversity of AMF communities in the soil. In 2004 and 2005, soil, plant, and root samples were taken on Triticum turgidum L. (durum) with preceding crops of Pisum sativum L. (pea), Lens culinaris Medik (lentil), Cicer arietinum L. (chickpea), Brassica napus L. (canola) or Triticum turgidum L. (durum). Although there were few differences in soil N and P levels, previous crop had a significant effect (p<0.05) on durum yields in both years. A previous crop of pea was associated with the highest yields, while the durum monocultures were lowest. Arbuscular mycorrhizal potential and colonization were significantly affected (p<0.05) by cropping history, but not consistently as a result of inclusion of a pulse crop. Phospholipid and neutralipid fatty acids (PLFA/NLFA) were completed to analyse the relative abundance of AMF (C16:1ù5), saprophytic fungi (C18:2ù6), and bacteria in the soil. The effect of treatment on the abundance of AMF, saprotrophic fungi and bacteria were not significant (p<0.05), but the changes over time were. These results demonstrate that although previous crop may play a role in microbial community structure, it is not the only influencing factor.

Title from first page of PDF document. Includes bibliographical references (p. 22-27).

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