Prairie Soils Research Articles

Inhibitory interaction networks among coevolved Streptomyces populations from prairie soils.

Soil microbes live within highly complex communities, where community composition, function, and evolution are the product of diverse interactions among community members. Analysis of the complex networks of interactions within communities has the potential to shed light on community stability, functioning, and evolution. However, we have little understanding of the variation in interaction networks among coevolved soil populations. We evaluated networks of antibiotic inhibitory interactions among sympatric Streptomyces communities from prairie soil. Inhibition networks differed significantly in key network characteristics from expectations under null models, largely reflecting variation among Streptomyces in the number of sympatric populations that they inhibited. Moreover, networks of inhibitory interactions within Streptomyces communities differed significantly from each other, suggesting unique network structures among soil communities from different locations. Analyses of tri-partite interactions (triads) showed that some triads were significantly over- or under- represented, and that communities differed in ‘preferred’ triads. These results suggest that local processes generate distinct structures among sympatric Streptomyces inhibition networks in soil. Understanding the properties of microbial interaction networks that generate competitive and functional capacities of soil communities will shed light on the ecological and coevolutionary history of sympatric populations, and provide a foundation for more effective management of inhibitory capacities of soil microbial communities.

Bacterial communities of soil and earthworm casts of native Palouse Prairie remnants and no-till wheat cropping systems

Earthworms are important ecosystem engineers and modify the physical and chemical properties of soils. However, less is known about how earthworms impact soil microbial communities. We compared bacterial communities of the bulk soil and earthworm casts in native prairie remnants and wheat cropped fields in the Palouse of eastern Washington using next-generation sequencing. Communities among prairie sites were similar, indicating a consistent prairie community. The bulk soil and earthworm casts of native prairie locations had higher richness compared to agricultural sites, but similar diversity. Diversity tended to be higher in bulk soil than earthworm casts in native prairies but not agricultural soils. In native prairies, earthworm casts were enriched in the families Caulobacteraceae, Cellulomonadaceae, Cytophagaceae, and Microbacteriaceae, and the genera Flavobacterium, Caulobacter, Burkholderia, Brevundimonas, compared to the bulk soil. In agricultural soils, Geodermatophilaceae, Flavobacterium and Pseudomonas were relatively more abundant in casts, whereas bulk soil harbored greater relative abundances of taxa related to Acidobacteria GP1. Casts from prairies had higher abundances of Actinobacteria, including Cellulomonas, Pseudonocardia, Geodermatophilaceae, and Propionibacteraceae, whereas casts from agricultural habitats were especially enriched in Flavobacterium and Pseudomonas. Fresh casts from Aporrectodea trapezoides from agricultural sites were highly enriched in Flavobacteriaceae, Pseudomonadaceae, Nocardioidaceae and Geodermatophilaceae and in OTUs related to Flavobacterium, Pseudomonas, and Bradyrhizobiaceae. Co-occurrence networks among communities from bulk soil and earthworm casts collected from agricultural fields were strikingly different than those from prairie soils and formed only two modules of co-occurring taxa, compared to 8–9 modules in the prairie soils, indicating a greater complexity of interactions. Networks from agricultural fields tended to have lower ratios of positive to negative edges (interactions) compared to prairie soils, suggesting more competition and antagonism among bacteria. Thus, the specific co-occurring taxa, as well as the aggregate structure of ecological interactions, are largely distinct between Palouse prairie soil communities versus those of earthworm casts in agricultural settings.

Late glacial aster prairie at the Aubrey Clovis site, North Texas, USA

Pollen analysis of pond and spring deposits at the Aubrey Clovis site in North Texas provides a 1300-year record of late glacial grassland vegetation from 17,200 to 15,900 cal years BP. Forty-six pollen taxa are identified in the well-preserved assemblages. The late glacial pollen record at the Aubrey site represents three environments: upland, riparian, and lacustrine-wetland. The pond-related sediments are dominated by 80% Poaceae pollen, an unusually high amount in pollen records; the spring tufa sediments are dominated by Cyperaceae. Cattail (Typha latifolia) and other wetland plants, including green algae Botryococcus, Pediastrum, and Chara were present. The riparian habitat of the wide late glacial alluvial valley had alder (Alnus), willow (Salix), cottonwood (Populus), and water elm (Planera aquatica). The upland vegetation was a treeless grassland with comparatively high amounts of Asteraceae-type pollen; it is therefore called the aster prairie. Quercus, Juniperus, Carya, Ulmus, Ambrosia, and Chenopodiaceae pollen are much less abundant than found in modern grassland pollen records. Small amounts of Artemisia, Pinus, and Picea pollen are present, a consequence of long-distance transport. Regional late glacial cool-wet climate produced moist prairie soils. The Cross Timbers oak forest that occurs near the site today had not yet formed. Dissimilarity analysis of the pollen data shows that the late glacial aster prairie has no analog with modern shortgrass, mixed-grass, or tallgrass prairies. In contrast, a favorable analog exists with fossil pollen data from a lower zone at Patschke Bog, central Texas, and Muscotah Marsh, northeastern Kansas, indicating that a grassland characterized by high amounts of Asteraceae pollen formed a unique late glacial vegetation type in the region, earlier in Texas and later in Kansas. Because of its chronology and location in the eastern Great Plains, the late glacial aster prairie may be ancestral to the modern tallgrass prairie.

Inhibitory and nutrient use phenotypes among coexisting Fusarium and Streptomyces populations suggest local coevolutionary interactions in soil.

Bacteria and fungi are key components of virtually all natural habitats, yet the significance of fungal-bacterial inhibitory interactions for the ecological and evolutionary dynamics of specific bacterial and fungal populations in natural habitats have been overlooked. More specifically, despite the broad consensus that antibiotics play a key role in providing a fitness advantage to competing microbes, the significance of antibiotic production in mediating cross-kingdom coevolutionary interactions has received relatively little attention. Here, we characterize reciprocal inhibition among Streptomyces and Fusarium populations from prairie soil, and explore antibiotic inhibition in relation to niche overlap among sympatric and allopatric populations. We found evidence for local adaptation between Fusarium and Streptomyces populations as indicated by significantly greater inhibition among sympatric than allopatric populations. Additionally, for both taxa, there was a significant positive correlation between the strength of inhibition against the other taxon and the intensity of resource competition from that taxon among sympatric but not allopatric populations. These data suggest that coevolutionary antagonistic interactions between Fusarium and Streptomyces are driven by resource competition, and support the hypothesis that antibiotics act as weapons in mediating bacterial-fungal interactions in soil.

Soil phosphorus bioavailability as influenced by long-term management and applied phosphorus source

Soil phosphorus (P) availability may be impacted by management practices, thereby affecting plant P uptake and plant response to P amendments. The aim of this study was to determine the effects of long-term management on soil P pools and to assess the response of P bioavailability, plant growth, and P uptake to mineral versus manure P treatments. Soils were collected from plots under organic (ORG), organic with composted manure (ORG + M), conventional (CONV), and restored prairie (PRA) management. Italian ryegrass (Lolium multiflorum L.) seedlings were grown in the greenhouse for 106 d in soils amended with various rates of manure or mineral P. The ORG soil had lower concentrations of labile P (resin-P and NaHCO3-P) compared with the CONV and PRA soils, as determined by sequential P fractionation prior to planting. Ryegrass biomass (root + shoot) and shoot P uptake from soils receiving no P were significantly lower for the ORG than all other management systems. Although apparent P use efficiency of the whole plant was increased by low P rate in the ORG management system, the source of applied P, manure > mineral, only influenced Olsen test P.

Access Matting Reduces Mixedgrass Prairie Soil and Vegetation Responses to Industrial Disturbance

Substantial interest exists in understanding the role of low-disturbance construction methods in mitigating industrial impacts to native grassland soils and vegetation. We assessed soil and vegetation responses to conventional high-disturbance sod-stripping and revegetation on sandy soils, and the alternative practice of low-disturbance access matting to provide a temporary work surface on sandy and loamy soils. Treatments were associated with high-voltage transmission tower construction during 2014 within the Mixedgrass Prairie. High-disturbance sites were hydroseeded in May of 2015, while low-disturbance sites recovered naturally. We assessed soil physical (bulk density, water infiltration) and chemical properties (organic matter, pH, and electrical conductivity) after construction and herbage biomass for three growing seasons. Sod-stripping led to 53% greater soil bulk density and 51% less organic matter than nondisturbed controls, while water infiltration increased by 32% in these high-sand (>80%) soils. In contrast, access matting led to minimal soil property changes regardless of the texture. While total herbage biomass was unaffected by all construction treatments, sod-stripping reduced grass biomass by 80% during the first growing season, which coincided with a 119% increase in forb mass. Root biomass (0-15 cm) also declined 77% with sod-stripping. Vegetation biomass on sites with access matting remained largely unaffected by the disturbance. Overall, low-disturbance construction methods using access matting were more effective than sod-stripping in mitigating the negative impacts of industrial development on Mixedgrass soil properties, as well as vegetation biomass, and are recommended as a best management practice during industrial disturbance.

Metaphenomic Responses of a Native Prairie Soil Microbiome to Moisture Perturbations.

Climate change is causing shifts in precipitation patterns in the central grasslands of the United States, with largely unknown consequences on the collective physiological responses of the soil microbial community, i.e., the metaphenome. Here, we used an untargeted omics approach to determine the soil microbial community's metaphenomic response to soil moisture and to define specific metabolic signatures of the response. Specifically, we aimed to develop the technical approaches and metabolic mapping framework necessary for future systematic ecological studies. We collected soil from three locations at the Konza Long-Term Ecological Research (LTER) field station in Kansas, and the soils were incubated for 15 days under dry or wet conditions and compared to field-moist controls. The microbiome response to wetting or drying was determined by 16S rRNA amplicon sequencing, metatranscriptomics, and metabolomics, and the resulting shifts in taxa, gene expression, and metabolites were assessed. Soil drying resulted in significant shifts in both the composition and function of the soil microbiome. In contrast, there were few changes following wetting. The combined metabolic and metatranscriptomic data were used to generate reaction networks to determine the metaphenomic response to soil moisture transitions. Site location was a strong determinant of the response of the soil microbiome to moisture perturbations. However, some specific metabolic pathways changed consistently across sites, including an increase in pathways and metabolites for production of sugars and other osmolytes as a response to drying. Using this approach, we demonstrate that despite the high complexity of the soil habitat, it is possible to generate insight into the effect of environmental change on the soil microbiome and its physiology and functions, thus laying the groundwork for future, targeted studies.IMPORTANCE Climate change is predicted to result in increased drought extent and intensity in the highly productive, former tallgrass prairie region of the continental United States. These soils store large reserves of carbon. The decrease in soil moisture due to drought has largely unknown consequences on soil carbon cycling and other key biogeochemical cycles carried out by soil microbiomes. In this study, we found that soil drying had a significant impact on the structure and function of soil microbial communities, including shifts in expression of specific metabolic pathways, such as those leading toward production of osmoprotectant compounds. This study demonstrates the application of an untargeted multi-omics approach to decipher details of the soil microbial community's metaphenotypic response to environmental perturbations and should be applicable to studies of other complex microbial systems as well.

Are two strategies better than one? Manipulation of seed density and soil community in an experimental prairie restoration

Restoration practitioners have a variety of practices to choose from when designing a restoration, and different strategies may address different goals. Knowledge of how to best use multiple strategies could improve restoration outcomes. Here, we examine two commonly suggested strategies in a single tallgrass prairie restoration experiment: increased forb sowing density and prairie soil inoculation. We designed a study with two different forb seeding densities. Within these densities, we transplanted seedlings into 1‐m2 plots that had been grown in either a whole prairie soil inoculum or sterilized prairie soil. After 4 years, we found positive effects of both high forb sowing density and inoculation treatments on the ratio of seeded to nonseeded plant cover in these plots, and negative effects of both treatments on nonseeded plant diversity. No effects of either treatment were seen on seeded plant diversity. Each strategy also affected the plant community in different ways: high forb sowing density increased seeded forb richness and decreased native nonseeded plant cover, while inoculation decreased non‐native cover, and tended to increase average successional stage of the community. These effects on restoration outcome were typically independent of each other, with the result that plots with both manipulations had the most positive effects on restoration outcomes. We thus advocate the combined use of these restoration strategies, and further studies which focus on both seeding and soil community manipulation in restoration.

Long‐term impacts of warming drive decomposition and accelerate the turnover of labile, not recalcitrant, carbon

AbstractWarming is altering the way soils function in ecosystems both directly by changing microbial physiology and indirectly by causing shifts in microbial community composition. Some of these warming‐driven changes are short term, but others may persist over time. Here, we took advantage of a long‐term (14 yr) warming experiment in a tallgrass prairie to tease apart the influence of short‐ and long‐term warming on litter decomposition. We collected soils originating from warmed and control plots and incubated them with a common litter substrate in a reciprocal design under elevated and ambient growth chamber temperatures. Litter decomposition was 40% higher in soils that were warmed in the field for 14 yr (long‐term warming) relative to soils derived from ambient plots. Short‐term warming in the laboratory had less of an impact on decomposition—decomposition increased by 12% under laboratory warming. Using a two‐pool soil carbon model to explore how different carbon pools may be responding, we found that long‐term warming accelerated the turnover of labile, not recalcitrant, carbon in these prairie soils—a result that is likely due to shifts in soil community activity/composition. Taken together, our results offer experimental evidence that warming‐induced changes in the soil community that occur over 14 yr of warming have long‐lasting effects on carbon turnover.

An online microbial data management system for poring over the equine microbiome

The soil bacteria diversity and corresponding environmental data made available here are from a 72-field plot experiment testing the effect of pulse frequency in nine wheat-based rotation systems, in the semiarid prairie. The data include sequences of the V6–V8 regions of bacterial 16S rDNA from soil and root extracts, generated using Roche GS FLX Titanium technology, and associated environmental data, specifically levels of soil organic carbon, total carbon, total nitrogen, total phosphorus, pH, electrical conductivity, and extractible sulfate sulfur, copper, iron, manganese, zinc, potassium, nitrate nitrogen, phosphate phosphorus, calcium, and magnesium in the 0–15 cm soil layer, and mineral nitrogen and phosphate in the 0–120 cm soil layer. The grain yield of wheat in the last (4th) phase of the crop rotation systems is also given. The data can be used in meta-analyses of the effect of pea, lentil and chickpea in wheat-based cropping systems on soil bacterial diversity or for monitoring the evolution of soil bacteria communities in cultivated prairie soils in the context of climate change. Samples were collected between 2012 and 2014.

Effect of Environmental Factors on the Abundance of Culturable Nitrate Reducing/Denitrifying Bacteria from Contaminated and Uncontaminated Tallgrass Prairie Soil

Various environmental factors have been proposed, such as soil moisture levels, carbon, and nitrate sources to affect the abundance of nitrate reducing (NR) and denitrifying (DN) bacteria. In this study, the strength of the association of the abundance of NR and DN bacteria with various environmental factors is estimated using multivariate statistics. Soil samples were collected from tallgrass prairie soils that had been contaminated with crude oil or brine (e.g. salt water) up to 10 years previously and from parallel uncontaminated sites. The abundance of culturable NR and DN bacteria in the soil samples was estimated by 5-tube MPN method using nitrate broth, while total petroleum hydrocarbons (TPH), sodium chloride, nitrate, and moisture were measured in the contaminated and the parallel uncontaminated sites. Viable heterotrophic bacteria and NR and DN bacteria from all sites were obtained from samples with a broad range of soil moisture (around 10-30% water/g soil) regardless of the source (e.g. site) of the isolates. Our results showed that the abundance of NR and DN bacteria from the contaminated sites was not less than that from the uncontaminated sites and reflected soil moisture, with greater bacterial numbers from wetter soils. Also, current remediation treatments (e.g. nitrate, hay, watering) of contaminated sites sometimes, but not consistently, were associated with greater abundance of NR and DN bacteria. Therefore, no long-term effect of contamination on the abundance of NR and DN bacteria was shown.

Phospholipid Fatty Acid Profiles of Soils under Variable Handling and Storage Conditions

Core Ideas Sample handling had profound and disproportionate effects on PLFA biomarkers. Gram positive and actinobacteria were not significantly affected by storage. Gram negative and fungal biomarkers were dramatically affected by storage. PLFA ratios significantly changed as a result of sample handling and storage. Interpretation of PLFA profiles is highly sensitive to sample handling. ABSTRACTPhospholipid fatty acid (PLFA) analysis is an increasingly popular method for estimating microbial biomass and assessing microbial community structure in soils. In particular, there is a strong interest in the use of PLFA microbial group ratios as benchmarks for soil health assessment and interpretation. Due to the sensitivity of PLFA biomarkers, the recommended procedure for sample handling involves immediate analysis of fresh, field‐moist soil, immediate lyophilization with freezer storage, or storage at –80°C. This protocol may not be practical under all circumstances, yet the effects of handling and storage conditions, and the implications for interpretation of PLFA biomarkers, are not fully understood. The primary objective of this study was to evaluate the effects of multiple sample handling and storage conditions on quantification and interpretation of PLFA biomarkers. A suite of soil properties were measured on 17 prairie soil samples, including PLFA analysis. Multiple processing and handling procedures were evaluated by splitting the soil samples and comparing PLFA profiles from (i) fresh soil, (ii) soil stored air‐dry for 7 and 14 d, (iii) soil stored field‐moist at room temperature for 7 and 14 d, and (iv) soil oven‐dried for 24 h at 105°C. All handling and storage procedures resulted in significant losses of PLFA biomarkers relative to fresh, lyophilized samples and microbial groups were disproportionately affected, leading to significant shifts in biomarker ratios. Overall, this study highlights the sensitivity of PLFA biomarkers, the importance of proper sample handling for PLFA analysis, and the potential for error and misinterpretation of PLFA data.

Solute Fluxes Through Restored Prairie and Intensively Managed Critical Zones in Nebraska and Iowa

Agricultural activities in the Midwestern United States have potentially altered geochemical fluxes within the critical zone (CZ) compared to native prairie systems that previously dominated the region. To quantify the impact of agricultural land use on soil and stream solute behavior, we studied two watersheds in the region: Glacier Creek Preserve (GCP) in eastern Nebraska and the Intensively Managed Landscapes Critical Zone Observatory (IML-CZO) in eastern Iowa. Both watersheds were initially under agricultural land use for over 100 years, but part of each watershed was restored to prairie 20 – 50 years ago. Soils at both sites formed in thick loess (≥6 m) overlying glacial till with similar mean annual temperatures (~10 °C) but slightly higher mean annual precipitation in Iowa (89 cm) compared to Nebraska (78 cm). At both sites, soil pore water and precipitation were collected every two to four weeks to measure anions, cations, and alkalinity; stream waters draining either restored prairie or agriculture were sampled similarly in Nebraska. Both soil moisture content and electrical conductivity were consistently higher in the upper one meter of agricultural soils compared to prairie soils in Nebraska, implying slower drainage and higher solute concentrations in the agricultural soils. At both sites, soil pore water Ca+2 and Mg+2 concentrations and annual fluxes were significantly higher in agricultural soils compared to restored prairie. Conversely, streams draining restored prairie have significantly higher Ca+2 and Mg+2 concentrations than the agricultural streams. Fluxes from agricultural streams, however, were higher than the prairie, pointing to a potential dilution effect of runoff from the agricultural land use. These observations lead to a conceptual model where deeply infiltrating water in restored prairie soils interacts with minerals present deeper in the soil before reaching the stream whereas in agricultural soils water does not infiltrate as deeply and thus experiences more shallow flowpaths to the stream. Furthermore, changes in geochemical and hydrologic fluxes have been realized in just a few decades since switching land use from agriculture to prairie. Thus, intense agricultural land use may alter soil function and solute transport to streams compared to critical zones hosting tallgrass prairie vegetation.

Legacies of afforestation on soil nematode community composition, structure, and diversity in a northern Canadian prairie

We examined how legacies of afforestation affect soil food webs using the composition, structure, and diversity of soil nematode communities along a prairie restoration chronosequence. Vegetation and soil nematode surveys were conducted across a restoration chronosequence of tree removal (2, 5, and 20 years) in a former plantation in Riding Mountain National Park, Canada, established on a Great Plains rough fescue prairie. Nematodes were extracted using sugar-gradient centrifugation, counted and assigned to feeding groups. Remaining plantation and recently restored prairies were characterized by bacterial feeding nematodes whereas the oldest restored prairie and control prairie were dominated by plant-root feeders. Nematode diversity did not reach the level observed in the prairie even 20 years following the removal of trees. Nematode community diversity and structure was strongly correlated with the composition of restored plant communities. Invasion of restored prairies by exotic grasses corresponded with a strong decline in the diversity of plant-root feeders. Legacies of afforestation can impact prairie soils years after trees have been removed and can lead to shifts in feeding structure and a loss of diversity in the soil food web. As grasslands continue to decline globally, considering soil faunal communities may help evaluate the outcomes of ecosystem restoration and maintain their key functions.

Methane emissions from rice across a soil organic matter gradient in Alfisols of Arkansas, USA

Quantifying greenhouse gas (GHG) emissions in agricultural settings has become critically important in determining the magnitude of agricultural impacts on global climate change. Methane (CH4) is a leading GHG emitted from rice (Oryza sativa L.) production and, since soil organic matter (SOM) serves as a substrate for methanogenesis, understanding the relationship between SOM and CH4 emissions will be essential for attenuating the excessive release of CH4 to the atmosphere from rice production. The objective of this field study was to evaluate the effects of SOM on CH4 emissions from rice grown under a full-season flood across several silt-loam soils in eastern Arkansas. Eight soils were collected from various locations around east-central Arkansas to represent a SOM gradient (22.1 to 51.0 Mg ha−1 in the top 10 cm) for this field study. Approximately 0.08 m3 of soil were placed in plastic bins that were buried in a single bay with the pure-line rice cultivar (‘LaKast’) transplanted into each bin and grown to harvest maturity under a full-season flood. Season-long, area-scaled CH4 emissions ranged from 63 to 1521 kg CH4-C ha−1 season−1 for in-situ and undisturbed field-plot soil and native prairie soil, respectively, and differed (P < 0.01) among the soils evaluated. Rice grown in soil from under a managed grassland, which had the largest SOM content in the top 10 cm, produced the second largest CH4 emissions (1166 kg CH4-C ha−1 season−1). Methane emissions increased linearly (P < 0.05) with increasing SOM and total carbon concentration (R2 = 0.81 and 0.85, respectively). Greater understanding of the influence of SOM on CH4 emissions is essential for assessing GHG impacts from rice production and for refining predictions of CH4 and total GHG emissions.

Auxin Herbicides and Pesticide Mixtures in Groundwater of a Canadian Prairie Province.

Groundwater samples were collected from piezometers and water table wells in both dryland and irrigated agricultural regions of Alberta, Canada, to examine the occurrence of pesticide mixtures. Fourteen current-use pesticides and two historical compounds were detected over a 3-yr sampling period. Pesticide mixtures were detected in ∼3% of the groundwater samples, and the frequency of detection increased from spring (1.5%) to summer (3.8%) and fall (4.8%). Pesticide mixtures always consisted of at least one of two auxin herbicides: 2,4-dichlorophenoxyacetic acid (2,4-D) or 2-methyl-4-chlorophenoxyacetic acid (MCPA). 19% of all samples contained a single pesticide, with auxin herbicides 2,4-D (7.3%), MCPA (4.4%), and clopyralid (3.9%) being most prevalent. We detected 2,4-D predominantly in the fall (72% of 2,4-D detections) and less in spring and summer (28%). We detected MCPA mostly in summer (85% of MCPA detections) and less in spring and fall (15%). Clopyralid was more evenly detected across spring (30%), summer (25%), and fall (45%). Since the auxin herbicides above are typically applied in summer, results suggest that each herbicide may have different mobility and persistence characteristics in prairie soils. Guidelines for Canadian Drinking Water Quality have been set for a range of individual pesticides, but not for pesticide mixtures. If Canada is to establish such guidelines, this study demonstrates that auxin herbicides should be prioritized. In addition, only 7 of the 16 compounds detected in this study have established maximum acceptable concentrations (MACs), excluding clopyralid, which was detected in all three sampling years.

Microbial Community Structure and Functional Potential in Cultivated and Native Tallgrass Prairie Soils of the Midwestern United States.

The North American prairie covered about 3.6 million-km2 of the continent prior to European contact. Only 1–2% of the original prairie remains, but the soils that developed under these prairies are some of the most productive and fertile in the world, containing over 35% of the soil carbon in the continental United States. Cultivation may alter microbial diversity and composition, influencing the metabolism of carbon, nitrogen, and other elements. Here, we explored the structure and functional potential of the soil microbiome in paired cultivated-corn (at the time of sampling) and never-cultivated native prairie soils across a three-states transect (Wisconsin, Iowa, and Kansas) using metagenomic and 16S rRNA gene sequencing and lipid analysis. At the Wisconsin site, we also sampled adjacent restored prairie and switchgrass plots. We found that agricultural practices drove differences in community composition and diversity across the transect. Microbial biomass in prairie samples was twice that of cultivated soils, but alpha diversity was higher with cultivation. Metagenome analyses revealed denitrification and starch degradation genes were abundant across all soils, as were core genes involved in response to osmotic stress, resource transport, and environmental sensing. Together, these data indicate that cultivation shifted the microbiome in consistent ways across different regions of the prairie, but also suggest that many functions are resilient to changes caused by land management practices – perhaps reflecting adaptations to conditions common to tallgrass prairie soils in the region (e.g., soil type, parent material, development under grasses, temperature and rainfall patterns, and annual freeze-thaw cycles). These findings are important for understanding the long-term consequences of land management practices to prairie soil microbial communities and their genetic potential to carry out key functions.

Tetracycline and Sulfonamide Antibiotic Resistance Genes in Soils From Nebraska Organic Farming Operations.

There is widespread agreement that agricultural antibiotic resistance should be reduced, however, it is unclear from the available literature what an appropriate target for reduction would be. Organic farms provide a unique opportunity to disentangle questions of agricultural antibiotic drug use from questions of antibiotic resistance in the soil. In this study, soil was collected from 12 certified organic farms in Nebraska, evaluated for the presence of tetracycline and sulfonamide resistance genes (n = 15 targets), and correlated to soil physical, chemical, and biological parameters. Tetracycline and sulfonamide antibiotic resistance genes (ARGs) were found in soils from all 12 farms, and 182 of the 196 soil samples (93%). The most frequently detected gene was tetG (55% of samples), followed by tet(Q) (49%), tet(S) (46%), tet(X) (30%), and tetA(P) (29%). Soil was collected from two depths. No differences in ARGs were observed based on soil depth. Positive correlations were noted between ARG presence and soil electrical conductivity, and concentrations of Ca, Na, and Mehlich-3 phosphorus. Data from this study point to possible relationships between selected soil properties and individual tetracycline resistance genes, including tet(O) which is a common target for environmental samples. We compared organic farm results to previously published data from prairie soils and found significant differences in detection frequency for 12 genes, eight of which were more commonly detected in prairie soils. Of interest, when tetracycline ARG results were sorted by gene mechanism, the efflux genes were generally present in higher frequency in the prairie soils, while the ribosomal protection and enzymatic genes were more frequently detected in organic farm soils, suggesting a possible ecological role for specific tetracycline resistance mechanisms. By comparing soil from organic farms with prairie soils, we can start to determine baseline effects of low-chemical input agricultural production practices on multiple measures of resistance.

Abundant Nonprotonated Aromatic and Oxygen-Bonded Carbons Make Humic Substances Distinct from Biopolymers

The nature of humic substances (HSs) extracted from soil organic matter and their distinction from degrading plant material has recently been called into question. Quantitative solid-state 13C nuclear magnetic resonance (NMR) analyses, in good agreement with elemental analysis, show that HSs are distinct from common biopolymers, refuting claims to the contrary made based on 1H-detected NMR spectra of the same standard peat humic acid as studied here. Aromatic carbons not bonded to hydrogen or oxygen, which are rare (≤10%) in common biomolecules, constitute a large fraction (28%–33%) of prairie soil and peat humic acids. Oxygen-bonded nonprotonated carbons such as aryl ketones, nonprotonated alkyl C–O, and abundant COOH groups are also characteristic of humic and fulvic acids but not observed in plant biopolymers. These distinctive structural differences between HSs and biopolymers challenge the recent proposal that HSs are unremarkable intermediates in a continuum of degrading biomolecules.

Phosphorus speciation in a prairie soil amended with MBM and DDG ash: Sequential chemical extraction and synchrotron-based XANES spectroscopy investigations

Sequential chemical extraction and synchrotron-based XANES spectroscopy techniques were used to identify P species in two ashes before and after addition to a prairie soil. The used ashes were: meat and bone meal ash (MBMA) and dried distillers grains ash (DDGA) plus mineral P fertilizer (MP) for comparison. Soil treated with MP contained higher content of resin-Pi and NaHCO3-Pi followed by DDGA and MBMA. The MBMA amended soil had the highest (47%) proportion of the soil P contained in recalcitrant HCl extractable fraction, reflecting more Ca-bound P present and being formed in soil after application. Analysis of both ashes with XANES spectroscopy before application to soil revealed that MBMA had strong spectral features consistent with hydroxyapatite (Ca5(PO4)3(OH)). DDGA exhibited spectral features consistent with a mixture of several Mg and K phosphate salts rather than a single mineral species. The distinctive features in the XANES spectra of both ashes largely disappeared after amendment to the soil, suggesting transformation to different P forms in the soil after application. It is also possible that the added amount of P to the studied soil via DDGS or MBMA was small enough so that P speciation is not different from the background P level.