Soil microbial community diversity and functionality as affected by integrated cropping-livestock systems in the Southern High Plains

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2012-12

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Abstract

Soil microorganisms constitute a small proportion of soil but are vital to the overall functioning and stability of ecosystems. The soil biota is frequently regarded as the “biological engine of the earth” as it performs many fundamental processes including nutrient cycling, soil structural dynamics and stability, degradation of pollutants, and regulation of plant communities. Introduction of molecular techniques has increased our analytic proficiency by providing greater taxonomic resolution and depth of coverage for microbial community assessments. Despite these advancements, one of the fundamental challenges in microbial ecology is to determine the relationship between community composition and function. Agricultural sustainability in the semi-arid Southern High Plains, U.S. is challenged by soils of inherently low fertility, depleting water resouces and highly variable and extreme weather conditions. Alternative agricultural management for the Southern High Plains region involves integrated livestock-crop production systems (ICL) which have shown to reduce water usage, fuel costs associated with irrigation, and potential to improve multiple soil quality parameters compared to monoculture crop production. The first objective of this research project focused on assessing microbial community structure and functionality under ICL compared to the typical practice of continuous cotton. The second objective was to evaluate the spatial distribution of the microbial community and the relationship of these microbial assemblages on the chemical composition of organic and mineral components. The first chapter contains background information on microbial diversity, community structure and their imporatance on ecosystem functionality as well as an overview of the major methods used to assess microbial structure and function. The second chapter combined physical, chemical, and molecular techniques to assess relationships between soil bacterial community structures and the quantity and quality of soil organic carbon (SOC) at the soil microenvironment scale (e.g., within different aggregate size-fractions). To accomplish this goal, soil samples from ICL and cotton systems were separated into macroaggregates (>250 μm), microaggregates (53-250 μm), and silt+clay (<53 μm) fractions and were analyzed for (1) bacterial diversity via pyrosequencing of the 16S rRNA gene and (2) SOC quantity and quality using a combustion method and mid-infrared diffuse reflectance spectroscopy (mid-IR), respectively. The mid-IR data revealed distinct spectral features indicating that these fractions were also distinguished by organic and mineral composition. Results from pyrosequencing showed that each soil microenvironment supported a distinct bacterial community, and that distributions of the less abundant bacterial phyla were more important for differentiating between communities in soil microenvironments. In the third chapter, mycorrhizal and saprophytic fungal populations (via fatty acid methyl ester profiles; FAME) and saprophytic fungal functionality (via FungiLog analysis) were evaluated under two ICL agroecosystems and a continuous cotton system at 0-5 and 5-20 cm depths. In addition to systems level comparisons, the effects of the vegetative components and grazing on fungal dynamics were evaluated. Abundance of saprophytic fungal FAMEs (10 to 26% of total FAMEs) and mycorrhizal FAMEs (2 to 24% of total FAMEs) were higher under ICLs compared to the continuous-cotton system at 0-5 cm. Overall, vegetation impacted the distribution of the fungal FAME markers, whereas the fungal saprophytic functionality was more sensitive to grazing. Perennial vegetation of ICLs was associated with increased fungal markers (saprophytic and mycorrhizal) as well as increased soil OM content. Higher fungal functional diversity was found under cotton, non-grazed perennial vegetation (with exception of bermudagrass) and the rotation under millet. Among the grazed perennial vegetation, bermudagrass showed the highest fungal FAMEs abundance and functional diversity values. These fungal improvements were also reflected in the highest OM content under this grass, potentially indicating improved sustainability under the OWB and bermudagrass agroecosystem. The fourth chapter describes results from microbial diversity according to pyrosequencing and enzymatic assays used to assess the effect of ICL systems and continuous cotton on bacterial and fungal diversity and (enzymatic) activity in these systems. Our data indicated that the microbial communities were distinct among the systems and vegetation, and the continuous cropping, whereas bacterial diversity indices, in general, were not impacted, reduced that fungal diversity. Lignin and cellulose degrading saprophytic fungi were prevalent under cotton containing systems, while perennial grasses were characterized by increased abundance of mycorrhizal fungi, implying that these two fungal groups play major roles in soil processes under these systems. Vegetation that had positive relationship with mycorrhizal and saprophytic fungal groups resulted in the highest enzymatic activity. This study also found positive correlation between certain bacterial and fungal taxa and soil properties such as total carbon, microbial biomass carbon and enzymatic activities. Investigation of microbial dynamics among agroecosystems at multiple spatial scales and taxonomic resolutions, provided insights to linking microbial community and functionality, and determining the overall impacts of agricultural management on the stability and resilience of these ecosystems.

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Keywords

Agroecosystems, Soil micorbial community, Grazing, Bacteria, Fungi

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