Effects of the Invasive Shrub Frangula alnus on Soil Microbial Communities and Biogeochemical Processes

The objective of this research was to determine the impacts of the invasive plant Frangula alnus, glossy buckthorn, on soil properties and microbial communities. Two studies were completed to achieve this objective. The first study examined the short-term impacts of F. alnus litter on soil properties and microorganims. In situ soil rings received the following aqueous treatments: deionized water, dextrose, cellulose, Quercus alba leaf extract, and F. alnus leaf extract (n = 7) and were sampled 1, 2, and 4 weeks after additions were made. In weeks 1 and 2, soil treated with F. alnus had higher total extractable N (NO3- + NH4+; TEN) than other treatments, which was likely due to enhanced N mineralization. In addition, changes to the microbial biomass C (MBC) to N (MBN) ratio in the F. alnus-treated soil indicated that microbial function had been altered. Overall, results suggest that F. alnus leaf litter has the capacity to alter soil properties and microbial function by stimulating N mineralization. The second study compared microbial communities and biogeochemical properties of soil at sites with F. alnus to non-invaded sites. Paired invaded/non-invaded sites (n = 11), including high (n = 6) and low (n = 5) density invasions, were sampled in spring, summer and fall of 2013. Paired t-tests revealed higher net N mineralization rates in invaded sites than non-invaded sites in summer, and in high density invaded sites than non-invaded sites during all sampling seasons. There was not, however, a corresponding increase in TEN at invaded sites. In addition, no differences between invaded and non-invaded sites were observed for soil C pools, MBC, MBC:MBN, and microbial community structure as assessed by terminal restriction fragment length polymorphisms. Overall, results suggest that F. alnus alters N cycling but has little impact on soil C pools.McIntire-Stennis Cooperative Forestry Research Program grant, the Gutgsell Family Foundation, and a Student Research Fund grant from the University of Wisconsin – Stevens Poin

Reporting the limits of detection and quantification for environmental DNA assays

Background: Environmental DNA (eDNA) analysis is increasingly being used to detect the presence and relative abundance of rare species, especially invasive or imperiled aquatic species. The rapid progress in the eDNA field has resulted in numerous studies impacting conservation and management actions. However, standardization of eDNA methods and reporting across the field is yet to be fully established, with one area being the calculation and interpretation of assay limit of detection (LOD) and limit of quantification (LOQ). Aims: Here, we propose establishing consistent methods for determining and reporting of LOD and LOQ for single‐species quantitative PCR (qPCR) eDNA studies. Materials & Methods/ Results: We utilize datasets from multiple cooperating laboratories to demonstrate both a discrete threshold approach and a curve‐fitting modeling approach for determining LODs and LOQs for eDNA qPCR assays. We also provide details of an R script developed and applied for the modeling method. Discussion/Conclusions: Ultimately, standardization of how LOD and LOQ are determined, interpreted, and reported for eDNA assays will allow for more informed interpretation of assay results, more meaningful interlaboratory comparisons of experiments, and enhanced capacity for assessing the relative technical quality and performance of different eDNA qPCR assays

Avian Influenza Virus RNA in Groundwater Wells Supplying Poultry Farms Affected by the 2015 Influenza Outbreak

During the 2015 outbreak of highly pathogenic avian influenza virus (HPAI) on poultry farms in the midwestern United States, concern was raised about the potential for HPAI to contaminate groundwater. Our study objective was to evaluate the occurrence of HPAI in the groundwater supply wells on 13 outbreak-affected poultry farms in Iowa and Wisconsin. We sampled 20 wells, six waste-storage lagoons, and one pond. Three wells and one lagoon were positive for the matrix gene indicative of influenza A virus. Using a semi-nested qPCR assay specific to the H5 HPAI outbreak strain, one well was H5-positive, matching the outbreak virus hemagglutinin gene. Matrix gene-positive samples analyzed for avian influenza virus (AIV) by cell culture and embryonating egg culture were negative. Seven wells were positive by PCR for a poultry-specific parvovirus, thus providing corroborating evidence of virus transport pathways between poultry fecal wastes and groundwater. Our data suggest it is possible for AIV to be transported to groundwater, and during an outbreak, the potential for poultry farm wells to become contaminated with AIV should be considered

Reporting the limits of detection and quantification for environmental DNA assays

Background: Environmental DNA (eDNA) analysis is increasingly being used to detect the presence and relative abundance of rare species, especially invasive or imperiled aquatic species. The rapid progress in the eDNA field has resulted in numerous studies impacting conservation and management actions. However, standardization of eDNA methods and reporting across the field is yet to be fully established, with one area being the calculation and interpretation of assay limit of detection (LOD) and limit of quantification (LOQ). Aims: Here, we propose establishing consistent methods for determining and reporting of LOD and LOQ for single‐species quantitative PCR (qPCR) eDNA studies. Materials & Methods/ Results: We utilize datasets from multiple cooperating laboratories to demonstrate both a discrete threshold approach and a curve‐fitting modeling approach for determining LODs and LOQs for eDNA qPCR assays. We also provide details of an R script developed and applied for the modeling method. Discussion/Conclusions: Ultimately, standardization of how LOD and LOQ are determined, interpreted, and reported for eDNA assays will allow for more informed interpretation of assay results, more meaningful interlaboratory comparisons of experiments, and enhanced capacity for assessing the relative technical quality and performance of different eDNA qPCR assays

Reporting the limits of detection and quantification for environmental DNA assays

Background: Environmental DNA (eDNA) analysis is increasingly being used to detect the presence and relative abundance of rare species, especially invasive or imperiled aquatic species. The rapid progress in the eDNA field has resulted in numerous studies impacting conservation and management actions. However, standardization of eDNA methods and reporting across the field is yet to be fully established, with one area being the calculation and interpretation of assay limit of detection (LOD) and limit of quantification (LOQ). Aims: Here, we propose establishing consistent methods for determining and reporting of LOD and LOQ for single‐species quantitative PCR (qPCR) eDNA studies. Materials & Methods/ Results: We utilize datasets from multiple cooperating laboratories to demonstrate both a discrete threshold approach and a curve‐fitting modeling approach for determining LODs and LOQs for eDNA qPCR assays. We also provide details of an R script developed and applied for the modeling method. Discussion/Conclusions: Ultimately, standardization of how LOD and LOQ are determined, interpreted, and reported for eDNA assays will allow for more informed interpretation of assay results, more meaningful interlaboratory comparisons of experiments, and enhanced capacity for assessing the relative technical quality and performance of different eDNA qPCR assays