EFFECTS OF AGRICULTURAL PRACTICES ON SOIL COMMUNITIES AND THEIR ASSOCIATED ECOSYSTEM SERVICES

To maximize crop yields, commodity crop production systems typically rely on inputs of fertilizers, pesticides, and irrigation; simplification of crop rotations (e.g., monocultures); and strategic use of soil disturbance (e.g., tillage, cultivation, etc.). While these practices are intended to optimize the soil conditions for crop development and reduce spatial and temporal variability in crop yield, they also impact soil biological diversity and the important agroecosystem services soil communities provide. Identification of management practices that are less prone to causing undesirable changes in the soil food web community are central to improving the sustainability of our agricultural systems. In this dissertation, I examined the effects of two agricultural management practices – conservation tillage and pesticide seed treatments – on the soil food web and soil-derived ecosystem services. The objective of my first study (Chapter 2) was to quantify the effects of zonal and uniform conservation tillage (ridge tillage vs. chisel plow) and strategic crop residue management (or soil functional zone management) on the abundance and diversity of the soil arthropod food web community inhabiting the crop row and inter-row zones in a maize-soybean system. In this two-year field experiment, I demonstrated that by using soil functional zone management, we can create unique zonation of the row and inter-row soil arthropod communities compared to uniform tillage. However, there were tradeoffs associated with this strategy, as the higher abundance of soil arthropods and more non-pest taxa associated with the crop rows under ridge tillage were offset by a more depauperate community inhabiting the crop inter-row compared to the uniformly tilled system. The objectives of Chapters 3 and 4 of this dissertation were to improve our understanding of how pesticide seed treatments (PST) with neonicotinoids affect soil food web communities and the soil functions they regulate. PST with neonicotinoids are widely used in commodity row cropping systems managed with conservation tillage to preemptively protect crop seeds and seedlings from soil-borne diseases and soil-dwelling insects. There is emerging evidence, however, that PST can negatively affect non-targeted organisms, yet its effects on soil arthropod communities are poorly understood. In Chapter 3, I demonstrate with a field experiment that PST with neonicotinoids can alter the abundance and diversity of non-targeted soil fauna spanning multiple trophic-levels with no detectable effect on herbivores – the guild that is the intended target of PST. Lastly, in Chapter 4, I demonstrate for the first time that the initial introduction of PST into a soil community results in dramatic changes in soil community abundance and diversity, while communities with prolonged histories of seed treatment exposure appear to be relatively unaffected by subsequent exposure. Together this research provides insight into how a specific set of conservation tillage strategies, and their often-associated pesticide technologies, impact the community of soil arthropods that are critical to the sustainability of agriculture

Increased Productivity of a Cover Crop Mixture Is Not Associated with Enhanced Agroecosystem Services

Cover crops provide a variety of important agroecological services within cropping systems. Typically these crops are grown as monocultures or simple graminoid-legume bicultures; however, ecological theory and empirical evidence suggest that agroecosystem services could be enhanced by growing cover crops in species-rich mixtures. We examined cover crop productivity, weed suppression, stability, and carryover effects to a subsequent cash crop in an experiment involving a five-species annual cover crop mixture and the component species grown as monocultures in SE New Hampshire, USA in 2011 and 2012. The mean land equivalent ratio (LER) for the mixture exceeded 1.0 in both years, indicating that the mixture over-yielded relative to the monocultures. Despite the apparent over-yielding in the mixture, we observed no enhancement in weed suppression, biomass stability, or productivity of a subsequent oat (Avena sativa L.) cash crop when compared to the best monoculture component crop. These data are some of the first to include application of the LER to an analysis of a cover crop mixture and contribute to the growing literature on the agroecological effects of cover crop diversity in cropping systems

Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer's disease

We identified rare coding variants associated with Alzheimer’s disease (AD) in a 3-stage case-control study of 85,133 subjects. In stage 1, 34,174 samples were genotyped using a whole-exome microarray. In stage 2, we tested associated variants (P<1×10-4) in 35,962 independent samples using de novo genotyping and imputed genotypes. In stage 3, an additional 14,997 samples were used to test the most significant stage 2 associations (P<5×10-8) using imputed genotypes. We observed 3 novel genome-wide significant (GWS) AD associated non-synonymous variants; a protective variant in PLCG2 (rs72824905/p.P522R, P=5.38×10-10, OR=0.68, MAFcases=0.0059, MAFcontrols=0.0093), a risk variant in ABI3 (rs616338/p.S209F, P=4.56×10-10, OR=1.43, MAFcases=0.011, MAFcontrols=0.008), and a novel GWS variant in TREM2 (rs143332484/p.R62H, P=1.55×10-14, OR=1.67, MAFcases=0.0143, MAFcontrols=0.0089), a known AD susceptibility gene. These protein-coding changes are in genes highly expressed in microglia and highlight an immune-related protein-protein interaction network enriched for previously identified AD risk genes. These genetic findings provide additional evidence that the microglia-mediated innate immune response contributes directly to AD development

Increased productivity of a cover crop mixture is not associated with enhanced agroecosystem services.

Cover crops provide a variety of important agroecological services within cropping systems. Typically these crops are grown as monocultures or simple graminoid-legume bicultures; however, ecological theory and empirical evidence suggest that agroecosystem services could be enhanced by growing cover crops in species-rich mixtures. We examined cover crop productivity, weed suppression, stability, and carryover effects to a subsequent cash crop in an experiment involving a five-species annual cover crop mixture and the component species grown as monocultures in SE New Hampshire, USA in 2011 and 2012. The mean land equivalent ratio (LER) for the mixture exceeded 1.0 in both years, indicating that the mixture over-yielded relative to the monocultures. Despite the apparent over-yielding in the mixture, we observed no enhancement in weed suppression, biomass stability, or productivity of a subsequent oat (Avena sativa L.) cash crop when compared to the best monoculture component crop. These data are some of the first to include application of the LER to an analysis of a cover crop mixture and contribute to the growing literature on the agroecological effects of cover crop diversity in cropping systems

Productivity of a cover crop mixture and component monocultures.

<p>Box plots showing variation around the median for shoot dry weight of five cover crops grown in monoculture and a mixture containing all five species in 2011 and 2012. The line within the box represents the median; the box represents 50% of the data; whiskers represent the 10^th and 90^th percentiles; n = 4.</p

Biomass of weeds that emerged from the ambient weed seed bank.

<p>Box plots showing variation around the median for ambient weed biomass in five cover crops grown in monoculture and a mixture containing all five species across the two study years. The line within the box represents the median; the box represents 50% of the data; whiskers represent the 10^th and 90^th percentiles; n = 8.</p

Biomass of surrogate weeds.

<p>Box plots showing variation around the median for surrogate weed biomass in five cover crops grown in monoculture and a mixture containing all five species in 2011 and 2012. The line within the box represents the median; the box represents 50% of the data; whiskers represent the 10^th and 90^th percentiles; n = 4.</p

Crop species used to create “surrogate weed community” subplots in 2011 and 2012.

<p>Crop species used to create “surrogate weed community” subplots in 2011 and 2012.</p

Variability in weed suppression in space and time.

<p>Coefficient of variation (CV) calculated across replicates (n = 4) and years (n = 2) for cover crop and ambient weed biomass in each cover crop monoculture and a mixture containing all five cover crop species.</p