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Supplemental material, Supplementary_material_Paulo for Soil and Human Health: Current Status and Future Needs by Eric C Brevik, Lindsey Slaughter, Bal Ram Singh, Joshua J Steffan, David Collier, Paul Barnhart and Paulo Pereira in Air, Soil and Water Research

Plants interact in myriad ways with microorganisms to influence ecosystem processes such as nutrient cycling, which can regulate ecosystem response to global change. One important plant-microbe symbiosis occurs between cool-season grasses and asexual fungal Epichloë endophytes, such as tall fescue (Schedonorus arundinaceus) and Epichloë coenophiala. Because the common toxic strain of the endophyte (CTE) harms grazing livestock, non-livestock toxic endophyte (NTE) strains have been developed and are increasingly deployed in pastures. Little is known about how these symbioses impact other plant-microbe interactions and microbe-mediated soil processes in grassland ecosystems. I conducted three studies to determine how E. coenophiala presence (+) or absence (−) and differences in endophyte strain affected plant-microbe-soil interactions both within tall fescue and in surrounding plants. I hypothesized that presence of CTE in tall fescue (CTE+) would suppress presence and/or activity of other microbial symbionts and related processes compared to E− tall fescue, and NTE+ tall fescue effects would be intermediate. My first field study examined how endophyte presence and strain in tall fescue influenced symbiotic biological nitrogen fixation (BNF) in red clover, biologically-fixed N uptake in tall fescue, and non-symbiotic BNF in soils. I found that tall fescue hosting different NTE+ strains utilized different amounts of biologically-fixed N. My second field study investigated how endophyte presence and strain impacted belowground mycorrhizal colonization within the same host plant. I found no significant differences in either AMF or dark septate endophyte (DSE) colonization in tall fescue in this study. In my third field study, I investigated how these belowground symbioses were potentially altered both by tall fescue-E. coenophiala genetics and future climate change. AMF functional structures such as arbuscules in roots and extraradical hyphae in soils were significantly affected by tall fescue genotype and endophyte status. I also found that some competitive symbiont interactions were ameliorated whereas others were exacerbated by future climate change conditions such as warming and added precipitation. Overall, the results of these studies suggest that genetically distinct E. coenophiala-tall fescue associations, through alteration of plant-microbe-soil interactions, will have divergent roles and long-term impacts on host-symbiont species interactions and nutrient cycling within pasture ecosystems.

The Southern High Plains (SHP) of the USA agriculture (crop and livestock production) is faced with many challenges such as limited water for irrigation, due to declining water levels of the Ogallala Aquifer. The insufficient and irregular rainfall, coupled with strong gusting winds that increase evapotranspiration worsens the situation. In addition, the soils in this region are highly degraded with < 1% soil organic matter (SOM). There’s a need for producers to adopt novel pasture-livestock management practices that are water efficient and that promote soil health and environmental sustainability such as the use of compost manure, use of legumes and limited irrigation coupled with grazing. Multiple research experiments were conducted in this thesis research to assess how alternative nutrient sources such as composted manure addition and legume forages (alfalfa and yellow sweetclover) interseeded with the WW-B. Dahl [WW-B. Dahl; Bothriochloa bladhii (Retz.), S.T. Blake perennial pasture impact soil biota and soil health in the SHP. In addition, we evaluated forage utilization practices: grazing contrasted with haying effect on soil’s biological, chemical and physical properties. Three pastures systems with different ages, past, and present management systems were evaluated. Key research conclusions include: Compost amendment increased total microbial biomass and changed the soil ecology as indicated by Non-metric multidimensional scaling (NMS) plots showing differences in microbial communities in compost and no compost treatments based on the selected phospholipids fatty acid (PLFA) biomarkers in fall 2018. Compost amendment increased soil total C, N, and SOM concentrations. Use of cattle manure could, therefore, be a sustainable and cost-effective way to enhance soil microbial communities, soil health and potentially increase forage yield in the SHP. The grass-legume mixture pasture system with long grazing history with no synthetic fertilization had higher total phospholipid fatty acid (PLFA), higher total C, N, SOM concentrations, and forage yield when contrasted with young grass-legume mixtures and pure stand grass pasture systems. The grass-legume mixture pasture system with long grazing history with no synthetic fertilization was ecologically different from young grass-legume mixtures and pure stand grass pasture. An interaction between year and grazing revealed that grazed treatment plots had a higher total carbon concentration indicating that grazing enhances soil organic carbon concentration. The grass-legume pasture had a higher N concentration than grass only suggesting that legume might have helped in N fixation. Overall, all the novel pasture management practices above, compost amendment, legume inclusion, and grazing are promising in enhancing soil microbial communities, promoting soil health and improving forage yield to sustain the economically important livestock industry in the SHP.

The Texas High Plains (THP) region is known for cotton (Gossypium hiristum L.) production and the Dust Bowl. Cotton production on the THP is massive, producing about 15% of USA cotton. With large areas under agricultural production, tillage is often used to manage the soil. Tillage is effective at controlling weeds on the THP and for preparing and making beds, however wind erosion is a problem on the THP, and often intensive tillage is not well suited to the sandy soil and semi-arid climate of the THP. Following the events of the Dust Bowl, conservation tillage and cover crop use has increased on the THP, with about 48% of land in Texas being under some form of the two practices in 2012. There are numerous benefits to conservation tillage and cover crop use, namely reduced wind erosion and greater water holding capacity of the soil on the THP. The potential to reduce or mitigate greenhouse gas (GHG) emissions from the soil and increases in cotton lint yield and fiber quality are also benefits that have been seen in other areas of the USA. Even with the potential benefits of conservation tillage and cover crop use regarding wind erosion, water holding capacity, mitigation of GHG emissions, and increases in cotton production, producers can still be reluctant to implement these practices due to a lack of information regarding the changes that occur in cotton production due to implementation of these systems on the THP. This study aimed to quantify the changes in carbon dioxide (CO2-C) and nitrous oxide (N2O-N) emissions, cotton lint yield, and cotton fiber quality within the first two years of implementation of no-tillage with (NTW) and without (NT) a winter cover crop compared to a conventional tillage (CT) system, and nitrogen (N) fertilizer application management within these tillage systems. In addition, changes in soil nutrient concentrations, cover crop N uptake and carbon (C) assimilation, microbial community structure, and cotton plant N uptake and partitioning were determined to provide a whole system evaluation of no-till and cover crop implementation on the THP. The fluxes of CO2-C and N2O-N were affected by the time of year in which the data was collected as well as a response to the addition of N fertilizer in some cases. Tillage affected CO2-C and N2O-N flux as well, with a generally greater flux occurring in the NTW system. Cumulative emissions of CO2-C and N2O-N were affected by N treatment in 2016 and CO2-C emissions were affected by tillage in 2017. Cotton lint yield differed between years due to climatic conditions that also affected the lint yield and fiber quality in 2017. The NTW system provided protection from high temperatures and winds early in the 2017 growing season, resulting in a better stand and more mature cotton with stronger fibers compared to NT and CT systems. Carbon assimilation in the wheat cover crop was greater than the amount of C lost due to the increase in CO2-C emissions in 2017, which may be a potential avenue of mitigation. Vegetative uptake of N was greater in treatments with a pre-season application of N fertilizer, while seed assimilation of N was generally greater in treatments with a mid-season application. Microbial abundance was greater in 2016 than in 2017, and a negative linear relationship was determined between fungal and bacterial abundance in 2017. Soil parameters were largely unchanged, although differences in pH, nitrate-N and sulfur due to tillage were determined, while total N was affected by the interaction of tillage and N treatment. Through this study, it was determined that the implementation of an NTW system will not directly mitigate CO2-C and N2O-N fluxes or gross cumulative emissions but may indirectly affect net CO2-C emissions through C sequestration in the wheat herbage mass. Use of a cover crop and no-till increased lint yield in the second year of this study due to climatic mitigation and should be continued to be examined in subsequent years to determine further effects on cotton lint yield and fiber quality with a changing climate. Overall, some trends were observed regarding no-tillage and cover crop use with differing N fertilizer timings, although rarely was there an interaction effect between them. The lack of interaction suggests the need for further study of cover crops and conservation tillage systems in subsequent years to better characterize the effects these systems have on soil and cotton growth dynamics on the THP.

The rapid decline in water supply for irrigation in the Texas High Plains is encouraging some growers to convert their irrigated cropland to dryland forages for livestock production. The vitality of the Ogallala Aquifer, a source for water supply for irrigation in the semi-arid Texas High Plains, is severely threatened owing to withdrawal rates that far exceed recharge rates. ‘WW-B.Dahl’ Old World bluestem [OWB, Bothriochloa bladhii (Retz) S.T. Blake] is a drought-tolerant grass in dryland and limited-irrigation conditions. Adoption of low water requiring perennial forages such as WW-B.Dahl OWB in forage-livestock production systems could potentially extend the economic life of irrigated row crops. This grass is reported to deter some insects such as red imported fire ant (RIFA, Solenopsis invicta Buren); but its effect on broader arthropod taxa and on soil microbial communities is unknown. Fewer horn flies (Haematobia irritans L.) have been casually observed on cattle (Bos taurus L.) grazing this grass compared to other grasses; however, observations were non-tested testimonials, and definitive data are unavailable. Visual ratings (1-5 scale) were compared for horn fly densities on cattle grazing two forage systems: grass-only (predominantly OWB) vs. grass-legume (OWB and alfalfa). Arthropod and soil microbial communities occurring in OWB, OWB-alfalfa (Medicago sativa L.), alfalfa, native mixed grass, and teff (Eragrostis tef (Zucc.) Trotter) pastures were characterized over 3 yr. I compared soil chemical and microbial properties in a Pullman clay-loam soil among OWB, OWB-alfalfa (Medicago sativa L.), alfalfa and native mixed-grass pastures at 0‒5 cm and 10‒15 cm depths in June and December of 2016. Qualitative analysis of chemical composition of essential oils of OWB was performed by gas chromatography (GC) and GC-mass spectrometry (MS) methods. I make the following major conclusions: • There was not a clear deterrence effect of WW-B.Dahl OWB on horn flies on cattle when compared to cattle grazing a grass-legume pasture system, which entailed spending less time on OWB. There is still a need for insecticidal treatment to control horn flies grazing OWB. • WW-B.Dahl OWB provides an unfavorable habitat for colonization by RIFA and harvester ants. Pastures containing OWB are expected to deter cattle health threats and grass stand decimation owing to absence of RIFA and harvester ants, respectively. • OWB appears to exhibit minor inhibitory effects on bees and other insect pollinators when compared to native mixed grasses and alfalfa pastures; however, pollinator populations are likely not threatened. • OWB did not clearly suppress the canopy-dwelling arthropods, while still hosting some arthropods of ecological significance; it appears that there is low risk of reducing overall arthropod diversity by wide adoption of OWB in the Texas High Plains. • The consistently greatest number of soil microbial communities and favorable soil biological properties in the OWB-alfalfa pastures compared to other forage types indicated that OWB had no suppressing effect on soil microorganisms, thus OWB-alfalfa is a promising pasture combination. • The consistently highest concentration of a single essential oil compound, Spiro [4.5] dec-6-en-8-one, 1,7-dimethyl-4-(1-methylethyl)-, out of 143 detected, prompts the need for further study of this compound to test its biological activity against RIFA and harvester ants. Much lower abundance was naphthalene, a known insect deterrent; however, its role as an insect deterrent in OWB is unknown without further study. In summary, results of these studies add to a growing body of work supporting the value of WW-B.Dahl OWB as a well-adapted perennial forage grass in the Southern Great Plains thanks to ant deterrence while maintaining overall insect diversity and hosting desirable soil microorganisms.

A variety of empirical models have been developed to determine soil water retention and hydraulic and thermal properties of unsaturated soils. The evaluation of the applicability of these empirical models for a variety of soils, soil, water, and agricultural management systems under different climatic or environmental conditions continue to be an important concern. These fundamental soil properties are critical for many studies of vadose zone hydrologic processes especially in the semi-arid Southern High Plains (SHP), where the increasing pressure on the depleting Ogallala Aquifer has stressed to develop sustainable alternatives, for example, forage-livestock systems, to the irrigation-dependent crop monocultures for the SHP agriculture. The overall objective of this study was to evaluate: (1) four widely used closed-form unimodal soil water retention curve (SWRC) models, i.e., Brooks and Corey (the BC model), van Genuchten (the VG1 and VG2 models), Kosugi (the K model), and Fredlund and Xing (the FX model) models to describe and to combine with pore-size distribution models with which to predict the unsaturated hydraulic conductivity function, and (2) four soil thermal conductivity (λ) predictive models, i.e., Johansen, Côté and Konrad, Balland and Arp, and Lu et al. models for pasture unsaturated soils with. Soil samples (at soil depths of 0-5, 5-10, 10-15, and 15-20 cm) collected from two semi-arid pastures (referred to as the east and west pasture area) in the SHP region under a variety of long-term drip-irrigated and dryland forage management systems were used to quantitatively compare the performance of the selected SWRC and λ models for pasture soils. Model parameters were estimated by fitting these SWRC and λ models to the measured data. Measured SWRCs showed the enhanced soil water retention behaviors (i.e., saturated water content, field capacity water content, plant available water) in pasture unsaturated soils (0-20 cm) under different management practices. Differences in the measured SWRCs between the west and east pasture soils are primarily attributed to the higher clay content of the latter. Notably, the observed organic matter content at the east pasture areas was also relatively higher. Differences in mean water contents of the top 0-5 cm unsaturated soils between treatments for both pastures were significant at lower matric potentials, i.e., in the dry part of SWRCs. No effect of pasture management practices on the saturated water content (s) and field capacity water content (fc) was observed, while significant differences for r or wilting point water content (at -15000 cm H2O) values were found between treatments both in the east and west pasture areas. In contrast with the west pasture with mostly sandy clay loam soils, no significant differences in PAW (plant available water) between treatments were found in the clay loam east pasture likely due to its higher clay and organic matter contents as well as relatively lower soil bulk density. All the selected SWRC models agreed well with measured data in the 0 to -15000 cm H2O range. However, the results of the goodness-of-fit statistics (i.e., RMSE, R2, R2adj, and AIC) suggested that the VG models (VG1 and VG2) performed best across the measured range (wet and dry parts of the SWRCs) of the soil water content. The  values within a treatment in both pasture areas varied with the changes in the soil water content in the 0 to -15000 cm H2O; however, no significant differences in  values (in the measured water range) were observed among treatments in both pastures. The results of the goodness-of-fit statistics (i.e., RMSE, R2, R2adj, and AIC) suggested that all the  models agreed well with measured data. This suggests that all four  models could provide reliable results across the soil water contents in the 0 to -15000 cm H2O range (i.e., water contents both in the wet and dry range) for semi-arid pasture soils under different pasture management practices.