Date of Award


Degree Name

MS in Environmental Sciences and Management


Natural Resources Management


College of Agriculture, Food, and Environmental Sciences


Charlotte Decock

Advisor Department

Natural Resources Management

Advisor College

College of Agriculture, Food, and Environmental Sciences


Plant-associated fungi such as arbuscular mycorrhizal fungi (AMF) have the potential to sequester carbon (C), improve soil aggregation, and promote plant health. Due to multiple benefits of AMF to plant and soil health, AMF has gained much attention leading to a rapidly expanding market in mycorrhizal bio-stimulants intended to improve crop yield, root development, and soil health in horticultural crops, including citrus. However, there is limited information on how to inoculate a mature citrus orchard, and how inoculation of a mature orchard with AMF affects C sequestration. In this study, we planted a cover crop inoculated with AMF in a mature lemon orchard and investigated the influence of the cover crop and AMF inoculation on C dynamics and the soil microbial community across the orchard floor. The experimental design was a Randomized Complete Block Design (RCBD) with three blocks and the following treatments applied in the alleyways: a cereal cover crop (Secale x Triticum L.) inoculated with AMF (Rhizophagus intraradices) at seeding, a cereal cover crop without inoculation, and a control where orchard alleys were left fallow. After two years of treatment implementation, soils were collected from each treatment plot from two functional locations, the tree row and the alley way, and two depth increments of 0-6 and 6-18 inches in order to asses soil C dynamics. To assess legacy effects of three years of practice implementation on soil C dynamics and microbial community structure, soils were collected at 0-6 inches depth from four functional locations: location one was between two trees on a berm, location two was in the transition section where the berm ends but no cover crop is grown, location three was on the edge of the cover cropped area (weeds in control plots), and location four was in the center of the alley row. AMF inoculation had no significant effects on soil C dynamics indicators such as total soil C, permanganate oxidazable carbon (POXC), mineralazable carbon (Min C), and soil aggregation. Likewise, AMF inoculation had no significant effect on microbial community biomass assesed with soil phospholipid fatty acids (PLFA) and neutral lipid fatty acids (NLFA). We attributed similarities between treatments to the non-inoculated cereal cover crop and weeds in the control treatment promoting native AMF. Across treatments, alley rows supported higher microbial community biomass and had higher total soil C (%), POXC (mg C/kg soil), and Min C (mg C/kg soil/day) than the tree row after three years of treatment implementation. After two years of treatment implementation, total soil C, Min C, and small macroaggregates (%) were higher in the topsoil in the cover cropped alley row compared to the topsoil in the three rows. We attribute the greater values for C cycling indicators and microbial abundance in the alley rows compared to the tree rows to positive impacts of tree prunings, weeds and cover crops and negative impacts of dry wet cycles in the alley versus tree rows, respectively. Correlation analysis showed that AMF and saprophytic fungi were significantly correlated with bacteria but not among themselves suggesting potential fungal-bacterial cooperation and niche differentiation between saprophytic fungi and AMF. In addition, correlation analysis showed that AMF and saprophytic fungi NLFA biomass was not significantly correlated with soil C indicators which contrasts other findings where fungi were key organisms in soil C accumulation. To summarize, AMF inoculation had no significant effect on soil C dynamics or the microbial community whereas differences in management between the tree and alley rows had a strong influence on soil C dynamics, microbial community biomass, and native AMF promotion in the lemon orchard.