The LTAR Cropland Common Experiment at the Texas Gulf.

Texas Gulf is one of the 18 regional sites that is part of the USDA-ARS Long-Term Agroecosystem Research (LTAR) Network and focuses on cropland and integrated grazing land research in Central Texas, addressing challenges posed by soil characteristics, climate variability, and urbanization. This paper provides brief site descriptions of the two Cropland Common Experiments being conducted in the Texas Gulf LTAR region, emphasizing conservation tillage practices and precision agriculture techniques. The plot-scale study is located in Temple, TX, at the USDA-ARS Grassland, Soil and Water Research Laboratory and examines conventional tillage, strip tillage, and no tillage practices. The field-scale study, located in Riesel, TX, at the USDA-ARS Riesel Watersheds, assesses the impact of no tillage, cover crops, fertility management, adaptive management, and precision conservation on crop yield, profitability, and environmental footprint. Key measurements include soil and plant analyses, greenhouse gas fluxes, runoff water quantity and quality, and field operations recorded with precision agriculture equipment. Despite challenges posed by urban encroachment, future research aims to incorporate new technologies, such as unmanned ground vehicles, to enhance sustainability and productivity of the agricultural landscape. These experiments provide valuable insights for stakeholders, contributing to the development of sustainable agricultural practices tailored to the unique challenges within the Texas Gulf LTAR region.

The LTAR-integrated grazing land common experiment at the Texas Gulf.

Extreme weather and climate events have become more frequent and directly affect the ecological structure and function of integrated grazing lands. While the Great Plains have experienced a long history of regular disturbances from drought and floods, grazing, and fires, the increased frequency and magnitude of these disturbances can reduce ecological resilience, largely depending on management practices. Alternative strategies designed to adaptively manage grazing land resources based on the ecology of the system should increase the resistance and resilience to disturbances when compared to prevailing practices. Determining the ecologic and economic value of alternative strategies will require long-term evaluations across large spatial scales. The Long-Term Agroecosystem Research Network has been established to evaluate the differences between alternative and prevailing practices among 18 strategically located sites and across decadal time scales throughout the continental United States. A key integrated grazing land site within this network is the Texas Gulf located at the Riesel Watersheds in the Blackland Prairie of Central Texas. At this study site, the differences between alternative and prevailing grazing management strategies are now being evaluated. The alternative strategy was designed using a combination of knowledge of the site and species ecology with modern-day tools and technologies. Alternatively, the prevailing practice implements a conventional year-round continuous grazing system with heavy reliance on hay and supplemental protein during winter. Results will provide grazing land managers with economically viable adaptive management choices for increasing ecological resilience following extreme and frequent disturbance events.

Heavy metals concentration in soils across the conterminous USA: Spatial prediction, model uncertainty, and influencing factors.

Assessment and proper management of sites contaminated with heavy metals require precise information on the spatial distribution of these metals. This study aimed to predict and map the distribution of Cd, Cu, Ni, Pb, and Zn across the conterminous USA using point observations, environmental variables, and Histogram-based Gradient Boosting (HGB) modeling. Over 9180 surficial soil observations from the Soil Geochemistry Spatial Database (SGSD) (n = 1150), the Geochemical and Mineralogical Survey of Soils (GMSS) (n = 4857), and the Holmgren Dataset (HD) (n = 3400), and 28 covariates (100 m × 100 m grid) representing climate, topography, vegetation, soils, and anthropic activity were compiled. Model performance was evaluated on 20 % of the data not used in calibration using the coefficient of determination (R2), concordance correlation coefficient (ρc), and root mean square error (RMSE) indices. Uncertainty of predictions was calculated as the difference between the estimated 95 and 5 % quantiles provided by HGB. The model explained up to 50 % of the variance in the data with RMSE ranging between 0.16 (mg kg-1) for Cu and 23.4 (mg kg-1) for Zn, respectively. Likewise, ρc ranged between 0.55 (Cu) and 0.68 (Zn), respectively, and Zn had the highest R2 (0.50) among all predictions. We observed high Pb concentrations near urban areas. Peak concentrations of all studied metals were found in the Lower Mississippi River Valley. Cu, Ni, and Zn concentrations were higher on the West Coast; Cd concentrations were higher in the central USA. Clay, pH, potential evapotranspiration, temperature, and precipitation were among the model's top five important covariates for spatial predictions of heavy metals. The combined use of point observations and environmental covariates coupled with machine learning provided a reliable prediction of heavy metals distribution in the soils of the conterminous USA. The updated maps could support environmental assessments, monitoring, and decision-making with this methodology applicable to other soil databases, worldwide.

Uncertainty in phosphorus fluxes and budgets across the US long-term agroecosystem research network.

Phosphorus (P) budgets can be useful tools for understanding nutrient cycling and quantifying the effectiveness of nutrient management planning and policies; however, uncertainties in agricultural nutrient budgets are not often quantitatively assessed. The objective of this study was to evaluate uncertainty in P fluxes (fertilizer/manure application, atmospheric deposition, irrigation, crop removal, surface runoff, and leachate) and the propagation of these uncertainties to annual P budgets. Data from 56 cropping systems in the P-FLUX database, which spans diverse rotations and landscapes across the United States and Canada, were evaluated. Results showed that across cropping systems, average annual P budget was 22.4 kg P ha-1 (range = -32.7 to 340.6 kg P ha-1 ), with an average uncertainty of 13.1 kg P ha-1 (range = 1.0-87.1 kg P ha-1 ). Fertilizer/manure application and crop removal were the largest P fluxes across cropping systems and, as a result, accounted for the largest fraction of uncertainty in annual budgets (61% and 37%, respectively). Remaining fluxes individually accounted for <2% of the budget uncertainty. Uncertainties were large enough that determining whether P was increasing, decreasing, or not changing was inconclusive in 39% of the budgets evaluated. Findings indicate that more careful and/or direct measurements of inputs, outputs, and stocks are needed. Recommendations for minimizing uncertainty in P budgets based on the results of the study were developed. Quantifying, communicating, and constraining uncertainty in budgets among production systems and multiple geographies is critical for engaging stakeholders, developing local and national strategies for P reduction, and informing policy.

Connecting soil characteristics to edge-of-field water quality in Ohio.

Soil health and water quality improvement are major goals of sustainable agricultural management systems, yet the connections between soil health and water quality impacts remain unclear. In this study we conducted an initial exploratory assessment of the relationships between soil chemical, physical, and biological properties and edge-of-field water quality across a network of 40 fields in Ohio, USA. Discharge, dissolved reactive P (DRP), total P (TP), and nitrate (NO3 ) losses associated with precipitation events via surface runoff and tile drainage were monitored. Agronomic soil tests and a suite of soil health indicators were measured, then predictive relationships between the field average soil properties and tile drainage and surface runoff discharge and DRP, TP, and nitrate loads were explored with random forest and multiple linear regression approaches. Among the soil health indicators, water extractable C and N were consistently found to be positively related to tile nitrate loads, but other soil health indicators had little or inconsistent importance for water quality impacts. Several other soil properties were important predictors, particularly soil P pools for surface and tile DRP and TP losses as well as Mehlich-3 (M3) extractable Fe and Al for surface and tile discharge. Thus, we did not observe strong evidence that soil health was associated with improved edge-of-field water quality across the edge-of-field monitoring network. However, additional studies are needed to definitively test the relationships between a broader array of soil health metrics and water quality outcomes.

Phosphorus sorption and desorption as affected by long-term cover cropping at two soil surface depths.

Phosphorus (P) loss from agricultural land is a persistent environmental challenge, and a better understanding of the impact of continuous cover crops (CCs) growth on soil P sorption and desorption characteristics is needed to inform mitigation strategies. This study investigated the impact of CC species on soil P pools, sorption characteristics, and dissolved reactive P (DRP) after 9 yr. Soil samples were collected at 0-to-2- and 2-to-4-cm soil depths from a silty clay loam Mollisol. Treatments included cereal rye (Secale cereal L.; CR), annual ryegrass (Lolium multiflorum, AR), oats/radish (Avena sativa L./Raphanus sativus L.; OR), and no CC (CN). A sorption experiment was done with varying P concentrations for 24 h equilibration, and sorption parameters were estimated using the Langmuir model. The DRP was estimated using sequential soil extraction by 0.01 M CaCl2 for 5 h. Long-term CC significantly decreased P sorption maximum but increased binding energy relative to CN. Annual ryegrass significantly decreased soil water extractable P, Mehlich 3 P, and degree of P saturation relative to OR and CN at the 0-to-2-cm depth. Annual ryegrass and CR significantly decreased desorbed DRP by an average of 42 and 45% relative to CN and OR, respectively, at the 0-to-2-cm depth. These results demonstrated that long-term grass species decreased the concentrations of labile P pools and desorbed DRP at the soil runoff interaction zone. Therefore, planting of AR and CR should be promoted in fields susceptible to runoff DRP losses.

Long-term performance of three mesophilic anaerobic digesters to convert animal and agro-industrial wastes into organic fertilizer.

Few studies have investigated the performance of anaerobic digestion (AD) to convert animal and agro-industrial wastes to organic fertilizers over a long-term field conditions. This paper studied three large-scale mesophilic digesters (D1eD3) over two years for their effects on feedstocks, which were dairy manure for D1 and D2 and co-digestion mixed manure and agro-industrial wastes for D3. Hydraulic retention times (HRT) were 9 d for D1, 12 d for D2, and 34 d for D3. Digester influent and effluent samples were taken every two months from the digesters and analyzed for pH, and concentrations of total solids (TS), ammonium nitrogen (NH4-N), total Kjeldahl nitrogen (TKN), total phosphorus (TP), and eight metals. The study revealed high variability in converting feedstock in the three digesters. Compared with their respective influent, the mean digester effluent pH decreased from 7.9 by 0.6 in D1 (p < 0.01) and by 0.3 in D2 (p < 0.01), but it increased from 6.1 by 1.8 in D3 (p < 0.01). The mean digester effluent TS increased from 3.4% by 0.1% (p > 0.05) in D1, but it decreased from 4.9% by 1.3% in D2 (p < 0.05) and from 12.3% by 4.8% in D3 (p < 0.01). All three digesters significantly increased NH4-N concentrations by 21.4 e81.8% (p < 0.05), but insignificantly changed TKN and TP concentrations (p > 0.05). Effects of AD on all metal concentrations were mixed and were insignificant (p > 0.05) because of large concentration variations. However, study of a ratio quotient (q Mg ) using magnesium (Mg) as the reference discovered accumulation of NH4-N, copper, potassium, and sodium, but loss of TKN, TP, iron, manganese, zinc, and calcium during AD for D2 and D3. The impact of AD conversion was closely related with types of feedstock (on pH) and HRT (on TS and NH4-N). The results of this study can assist in developing strategies for cleaner production using AD in an environmentally sustainable manner.

Unique age-related transcriptional signature in the nervous system of the long-lived red sea urchin Mesocentrotus franciscanus.

The red sea urchin, Mesocentrotus franciscanus, is one the earth's longest-lived animals, reported to live more than 100 years with indeterminate growth, life-long reproduction and no increase in mortality rate with age. To gain insight into mechanisms associated with longevity and negligible senescence, age-related transcriptional profiles were examined in tissues of the red sea urchin. Genome-wide transcriptional profiling using RNA-Seq revealed few age-related changes in gene expression in muscle and esophagus tissue. In contrast, radial nerve showed an unexpected level of complexity with the expression of 3,370 genes significantly altered more than two-fold with age, including genes involved in nerve function, signaling, metabolism, transcriptional regulation and chromatin modification. There was an age-related upregulation in expression of genes involved in synaptogenesis, axonogenesis and neuroprotection suggesting preservation of neuronal processes with age. There was also an upregulation in expression of positive regulators and key components of the AMPK pathway, autophagy, proteasome function, and the unfolded protein response. This unique age-related gene expression profile in the red sea urchin nervous system may play a role in mitigating the detrimental effects of aging in this long-lived animal.

Conservation implications of fish-habitat relationships in channelized agricultural headwater streams.

Channelized agricultural headwater streams are common throughout agricultural watersheds in the midwestern United States. Understanding fish-habitat relationships within these streams will provide information that can assist with developing conservation and restoration strategies for these degraded streams. From spring 2006 to fall 2010, we collected fishes and measured riparian habitat, instream habitat, and water chemistry variables from seven sites in Cedar Creek, Indiana, and 14 sites in Upper Big Walnut Creek, Ohio. We found that fish community structure was more strongly correlated with instream habitat than riparian habitat or water chemistry in both watersheds. We also observed interrelationships among instream habitat, watershed size, and fish communities within both watersheds that suggest that the hydrological changes that occur with increasing watershed size are the underlying factor for fish community changes that occur with increasing watershed size. Our results suggest that conservation and restoration efforts within channelized agricultural headwater streams in the midwestern United States, where nutrients and herbicide concentrations are low, need to address physical habitat degradation to positively influence fish community structure.

The Role of Field-Scale Management on Soil and Surface Runoff C/N/P Stoichiometry.

Agricultural runoff is an important contributor to water quality impairment. This study was conducted to evaluate the potential role of field-scale management on carbon (C), nitrogen (N), and phosphorus (P) stoichiometry in soils and runoff from agricultural fields. Cultivated and pasture fields at the Riesel watersheds in central Texas were used for this analysis, and nutrients were transformed to evaluate relative to the Redfield ratio (106 C/16 N/1 P). Using the Redfield ratio, all soil samples were P depleted relative to C and N. The majority of stormflow and baseflow runoff samples contained 9 to 19% Redfield N relative to C and P. Shifting from inorganic fertilizer application to poultry litter as a fertilizer source resulted in increased absolute C, N, and P concentrations in stormflow and baseflow runoff. Increasing rates of poultry litter application increased the Redfield P relative to Redfield C, whereas Redfield N remained relatively constant at roughly 9 to 11% in stormflow runoff from cultivated fields. This study shows how land use and management can affect C/N/P stoichiometry in stormflow and baseflow runoff.

Targeted gene sequencing in 6994 individuals with neurodevelopmental disorder with epilepsy.

PURPOSE: We aimed to gain insight into frequencies of genetic variants in genes implicated in neurodevelopmental disorder with epilepsy (NDD+E) by investigating large cohorts of patients in a diagnostic setting. METHODS: We analyzed variants in NDD+E using epilepsy gene panel sequencing performed between 2013 and 2017 by two large diagnostic companies. We compared variant frequencies in 6994 panels with another 8588 recently published panels as well as exome-wide de novo variants in 1942 individuals with NDD+E and 10,937 controls. RESULTS: Genes with highest frequencies of ultrarare variants in NDD+E comprised SCN1A, KCNQ2, SCN2A, CDKL5, SCN8A, and STXBP1, concordant with the two other epilepsy cohorts we investigated. In only 46% of the analyzed 262 dominant and X-linked panel genes ultrarare variants in patients were reported. Among genes with contradictory evidence of association with epilepsy, CACNB4, CLCN2, EFHC1, GABRD, MAGI2, and SRPX2 showed equal frequencies in cases and controls. CONCLUSION: We show that improvement of panel design increased diagnostic yield over time, but panels still display genes with low or no diagnostic yield. With our data, we hope to improve current diagnostic NDD+E panel design and provide a resource of ultrarare variants in individuals with NDD+E to the community.

Effects of wet corn distiller's grains with solubles and nonprotein nitrogen on feeding efficiency, growth performance, carcass characteristics, and nutrient losses of yearling steers12.

Wet distiller's grains with solubles (WDGS) are a common by-product feedstuff generated by the grain-ethanol industry, and it is used extensively by the cattle feeding industry. Distillers grains are typically high in protein; however, the protein in WDGS has a low ruminal degradability, and thus may result in a deficiency of RDP in the diet even when dietary CP concentrations are high. Assessment of the RDP needs in diets containing WDGS is needed to aid the cattle feeding industry in managing feed costs and potential environmental issues. To that end, we conducted 2 feeding studies to evaluate the supplemental RDP requirements of beef cattle fed steam-flaked corn-based finishing diets. In Exp. 1, 525 yearling steers (initial body weight = 373 ± 13 kg) received treatments in a 2 × 3 + 1 factorial. Dietary factors included WDGS (15 or 30% of DM) and nonprotein N (NPN; 0, 1.5, or 3.0% of DM) from urea (0, 0.52, and 1.06%). The control diet without WDGS contained 3.0% NPN (1.06% urea) and cottonseed meal. Diets were formulated to have equal crude fat concentrations. Overall gain efficiency among steers fed 15% WDGS was greatest for 1.5% NPN and least for 0% NPN (P = 0.07, quadratic), whereas gain efficiency decreased linearly (P < 0.09) as NPN increased in the 30% WDGS diets. Dressing percent was greater (P < 0.01) for the Control diet than for 15 or 30% WDGS. In Exp. 2, 296 steer calves (initial BW = 344 ± 12 kg) were fed 1 of 4 experimental diets that included a Control diet without WDGS (contained 3% NPN from urea, and cottonseed meal) and 15% WDGS diets with either 1.50, 2.25, or 3.00% NPN (0.52, 0.78, and 1.04% urea, respectively, on a DM basis). Overall gain efficiency on either a live or carcass-adjusted basis was not different among treatments (P > 0.15). Dietary NPN concentration did not influence growth performance (P > 0.21). Increasing dietary WDGS concentration resulted in decreasing (P < 0.05) diet digestibility (determined with an internal marker) and increasing (P < 0.05) N volatilization losses (determined by diet and manure N:P ratio); however, the effects of NPN level on digestibility and N losses were somewhat inconsistent across experiments. Results suggest that optimum performance for cattle fed 15% WDGS occurred when the diet contained between 1.5 and 2.25% NPN. However, no supplemental NPN was needed to support optimum performance in diets containing 30% WDGS.

Transforming soil phosphorus fertility management strategies to support the delivery of multiple ecosystem services from agricultural systems.

Despite greater emphasis on holistic phosphorus (P) management, current nutrient advice delivered at farm-scale still focuses almost exclusively on agricultural production. This limits our ability to address national and international strategies for the delivery of multiple ecosystem services (ES). Currently there is no operational framework in place to manage P fertility for multiple ES delivery and to identify the costs of potentially sacrificing crop yield and/or quality. As soil P fertility plays a central role in ES delivery, we argue that soil test phosphorus (STP) concentration provides a suitable common unit of measure by which delivering multiple ES can be economically valued relative to maximum potential yield, in $ ha-1 yr-1 units. This value can then be traded, or payments made against one another, at spatio-temporal scales relevant for farmer and national policy objectives. Implementation of this framework into current P fertility management strategies would allow for the integration and interaction of different stakeholder interests in ES delivery on-farm and in the wider landscape. Further progress in biophysical modeling of soil P dynamics is needed to inform its adoption across diverse landscapes.

Phosphorus and nitrogen limitation and impairment of headwater streams relative to rivers in Great Britain: A national perspective on eutrophication.

This study provides a first national-scale assessment of the nutrient status of British headwater streams within the wider river network, by joint analysis of the national Countryside Survey Headwater Stream and Harmonised River Monitoring Scheme datasets. We apply a novel Nutrient Limitation Assessment methodology to explore the extent to which nutrients may potentially limit primary production in headwater streams and rivers, by coupling ternary assessment of nitrogen (N), phosphorus (P), and carbon (C) depletion, with N:P stoichiometry, and threshold P and N concentrations. P limitation was more commonly seen in the rivers, with greater prevalence of N limitation in the headwater streams. High levels of potential P and N co-limitation were found in the headwater streams, especially the Upland-Low-Alkalinity streams. This suggests that managing both P and N inputs may be needed to minimise risks of degradation of these sensitive headwater stream environments. Although localised nutrient impairment of headwater streams can occur, there were markedly lower rates of P and N impairment of headwater streams relative to downstream rivers at the national scale. Nutrient source contributions, relative to hydrological dilution, increased with catchment scale, corresponding with increases in the extent of agricultural and urban land-use. The estimated nutrient reductions needed to achieve compliance with Water Framework Directive standards, and to reach limiting concentrations, were greatest for the Lowland-High-Alkalinity rivers and streams. Preliminary assessments suggest that reducing P concentrations in the Lowland-High-Alkalinity headwater streams, and N concentrations in the Upland-Low-Alkalinity rivers, might offer greater overall benefits for water-quality remediation at the national scale, relative to the magnitude of nutrient reductions required. This approach could help inform the prioritisation of nutrient remediation, as part of a directional approach to water quality management based on closing the gaps between current and target nutrient concentrations.

Rare genetic variants in the endocannabinoid system genes CNR1 and DAGLA are associated with neurological phenotypes in humans.

Rare genetic variants in the core endocannabinoid system genes CNR1, CNR2, DAGLA, MGLL and FAAH were identified in molecular testing data from 6,032 patients with a broad spectrum of neurological disorders. The variants were evaluated for association with phenotypes similar to those observed in the orthologous gene knockouts in mice. Heterozygous rare coding variants in CNR1, which encodes the type 1 cannabinoid receptor (CB1), were found to be significantly associated with pain sensitivity (especially migraine), sleep and memory disorders-alone or in combination with anxiety-compared to a set of controls without such CNR1 variants. Similarly, heterozygous rare variants in DAGLA, which encodes diacylglycerol lipase alpha, were found to be significantly associated with seizures and neurodevelopmental disorders, including autism and abnormalities of brain morphology, compared to controls. Rare variants in MGLL, FAAH and CNR2 were not associated with any neurological phenotypes in the patients tested. Diacylglycerol lipase alpha synthesizes the endocannabinoid 2-AG in the brain, which interacts with CB1 receptors. The phenotypes associated with rare CNR1 variants are reminiscent of those implicated in the theory of clinical endocannabinoid deficiency syndrome. The severe phenotypes associated with rare DAGLA variants underscore the critical role of rapid 2-AG synthesis and the endocannabinoid system in regulating neurological function and development. Mapping of the variants to the 3D structure of the type 1 cannabinoid receptor, or primary structure of diacylglycerol lipase alpha, reveals clustering of variants in certain structural regions and is consistent with impacts to function.

Phosphorus Availability in Western Lake Erie Basin Drainage Waters: Legacy Evidence across Spatial Scales.

The Western Lake Erie Basin (WLEB) was inundated with precipitation during June and July 2015 (two to three times greater than historical averages), which led to significant nutrient loading and the largest in-lake algal bloom on record. Using discharge and concentration data from three spatial scales (0.18-16,000 km), we contrast the patterns in nitrate (NO-N) and dissolved reactive phosphorus (DRP) concentration dynamics and discuss potential management implications. Across all scales, NO-N concentration steadily declined with each subsequent rainfall event as it was flushed from the system. In contrast, DRP concentration persisted, even on soils at or below agronomic P levels, suggesting that legacy P significantly contributes to nutrient loads in the WLEB. These findings highlight the need to revisit current P fertility recommendations and soil testing procedures to increase P fertilizer use efficiency and to more holistically account for legacy P.

Increased Soluble Phosphorus Loads to Lake Erie: Unintended Consequences of Conservation Practices?

Cumulative daily load time series show that the early 2000s marked a step-change increase in riverine soluble reactive phosphorus (SRP) loads entering the Western Lake Erie Basin from three major tributaries: the Maumee, Sandusky, and Raisin Rivers. These elevated SRP loads have been sustained over the last 12 yr. Empirical regression models were used to estimate the contributions from (i) increased runoff from changing weather and precipitation patterns and (ii) increased SRP delivery (the combined effects of increased source availability and/or increased transport efficiency of labile phosphorus [P] fractions). Approximately 65% of the SRP load increase after 2002 was attributable to increased SRP delivery, with higher runoff volumes accounting for the remaining 35%. Increased SRP delivery occurred concomitantly with declining watershed P budgets. However, within these watersheds, there have been long-term, largescale changes in land management: reduced tillage to minimize erosion and particulate P loss, and increased tile drainage to improve field operations and profitability. These practices can inadvertently increase labile P fractions at the soil surface and transmission of soluble P via subsurface drainage. Our findings suggest that changes in agricultural practices, including some conservation practices designed to reduce erosion and particulate P transport, may have had unintended, cumulative, and converging impacts contributing to the increased SRP loads, reaching a critical threshold around 2002.

Metagenomic analysis of medicinal Cannabis samples; pathogenic bacteria, toxigenic fungi, and beneficial microbes grow in culture-based yeast and mold tests.

Background: The presence of bacteria and fungi in medicinal or recreational Cannabis poses a potential threat to consumers if those microbes include pathogenic or toxigenic species. This study evaluated two widely used culture-based platforms for total yeast and mold (TYM) testing marketed by 3M Corporation and Biomérieux, in comparison with a quantitative PCR (qPCR) approach marketed by Medicinal Genomics Corporation. Methods: A set of 15 medicinal Cannabis samples were analyzed using 3M and Biomérieux culture-based platforms and by qPCR to quantify microbial DNA. All samples were then subjected to next-generation sequencing and metagenomics analysis to enumerate the bacteria and fungi present before and after growth on culture-based media. Results: Several pathogenic or toxigenic bacterial and fungal species were identified in proportions of >5% of classified reads on the samples, including Acinetobacter baumannii, Escherichia coli, Pseudomonas aeruginosa, Ralstonia pickettii, Salmonella enterica, Stenotrophomonas maltophilia, Aspergillus ostianus, Aspergillus sydowii, Penicillium citrinum and Penicillium steckii. Samples subjected to culture showed substantial shifts in the number and diversity of species present, including the failure of Aspergillus species to grow well on either platform. Substantial growth of Clostridium botulinum and other bacteria were frequently observed on one or both of the culture-based TYM platforms. The presence of plant growth promoting (beneficial) fungal species further influenced the differential growth of species in the microbiome of each sample. Conclusions: These findings have important implications for the Cannabis and food safety testing industries.

Quantifying Attachment and Antibiotic Resistance of from Conventional and Organic Swine Manure.

Broad-spectrum antibiotics are often administered to swine, contributing to the occurrence of antibiotic-resistant bacteria in their manure. During land application, the bacteria in swine manure preferentially attach to particles in the soil, affecting their transport in overland flow. However, a quantitative understanding of these attachment mechanisms is lacking, and their relationship to antibiotic resistance is unknown. The objective of this study is to examine the relationships between antibiotic resistance and attachment to very fine silica sand in collected from swine manure. A total of 556 isolates were collected from six farms, two organic and four conventional (antibiotics fed prophylactically). Antibiotic resistance was quantified using 13 antibiotics at three minimum inhibitory concentrations: resistant, intermediate, and susceptible. Of the 556 isolates used in the antibiotic resistance assays, 491 were subjected to an attachment assay. Results show that isolates from conventional systems were significantly more resistant to amoxicillin, ampicillin, chlortetracycline, erythromycin, kanamycin, neomycin, streptomycin, tetracycline, and tylosin ( < 0.001). Results also indicate that isolated from conventional systems attached to very fine silica sand at significantly higher levels than those from organic systems ( < 0.001). Statistical analysis showed that a significant relationship did not exist between antibiotic resistance levels and attachment in from conventional systems but did for organic systems ( < 0.001). Better quantification of these relationships is critical to understanding the behavior of in the environment and preventing exposure of human populations to antibiotic-resistant bacteria.

The Atlantic salmon genome provides insights into rediploidization.

The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (Salmo salar), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes.