A preliminary investigation of wild pig (Sus scrofa) impacts in water quality.

The United States, particularly the southern portion, has recently suffered drastic population expansion of wild pigs causing destruction of prime farmland. An associated concern, which has been understudied, is the potential transfer of nutrients and pathogens to surface water. This study aimed to identify the abiotic and biotic impacts of captive wild pigs on water quality, including nutrients, fecal indicator and pathogenic bacteria, and antimicrobial resistance. Overall, the study demonstrated that wild pigs harbored Salmonella spp., Campylobacter spp., Escherichia coli, and Clostridium perfringens, which were found in water runoff collected directly beneath the hog paddock, often 2 log10 greater than above-paddock levels. However, the impacts to downstream water quality were limited, perhaps because of a relatively large riparian buffer between the paddock and surface water. A higher rate of ammonium concentration changes over time was detected in the runoff water below the paddock; additionally, microbial releases detected in runoff were also time dependent, possibly associated with increasing pig numbers. Antibiotic resistance was generally not associated with the wild pigs. Antibiotic resistance genes were found in upstream as well as downstream surface water, suggesting that nonpoint sources of microbial contamination were present. Interestingly, intI1 levels were greater in below-paddock runoff by nearly 2 log10 . Overall, it appears that wild pigs potentially pose a threat to water quality but only if they have direct access to the water. Pathogen, fecal indicator bacteria, and some nutrient release were significantly associated with wild pigs, but riparian buffers limited water quality impairment.

Bacterial Community Structure Recovery in Reclaimed Coal Mined Soil under Two Vegetative Regimes.

Coal mining can be deleterious to the soil physical and chemical makeup, but also to the soil microbial community. Effectively, the removal of nearly all organic matter from the upper soil horizons reduces the effectiveness of any soil to support vegetation, and up until recently, microbial community parameters were not considered in the successful reclamation of overburden. Thus, our study proposes to measure the uncultivated bacterial community using 16S ribosomal RNA (rRNA) high-throughput sequencing in a chronosequence of reclaimed overburden in Mississippi. The study sites comprised samplings of pasture and wooded reclamation sites consisting of 1 to 13 yr post reclamation time, as well as reference sites. Overall, the primary driver of bacterial community dynamics was vegetative cover, although time also influenced dynamics. Richness estimations for operational taxonomic units (OTUs) showed that recently reclaimed (∼1 yr) and Pasture sites were more OTU rich with levels of >1400 compared with reference site levels of ∼1000. Diversity levels also followed a similar trend. Community structure typically differed between time points and vegetative cover; however, membership was similar between sites and reference, indicating that new communities still shared some membership from the previous community. Overall, physicochemical properties trended toward more positive for soil health as time progressed, but bacterial community recovery was still not structurally recovered, although richness and diversity values exceeded reference. Overall, this study demonstrated that mine reclamation using pasture and/or wood restoration can reestablish the bacterial community to approximate reference conditions, but vegetation is still the dominating environmental factor dictating microbial community.

Effects of Low-Grade Weirs on Soil Microbial Communities in Agricultural Drainage Ditches.

Agricultural fertilizer application throughout the Mississippi River basin has been identified as a major source of N pollution to the Gulf of Mexico. Using best management practices, such as low-grade weirs, has been identified as a potential solution to mitigate nutrient loads in agricultural runoff. This study assessed impacts of weir implementation in four agricultural drainage ditches (three with weirs and one control site) in the Mississippi Delta. Soil samples collected from field locations in spring 2013 were analyzed for denitrifier abundance using genes (16s ribosomal RNA [rRNA] genes, , , and ) via quantitative polymerase chain reaction (qPCR), microbial community profiles via terminal-restriction fragment length polymorphism (T-RFLP) of 16s rRNA genes, soil parameters (C, N, and moisture), and vegetation presence at sample locations. Gene quantification was successful, except for , which was found below detection limits (5000 gene copies g soil). Distance from weirs was negatively correlated with 16S rRNA genes and soil moisture, and soil moisture was positively correlated with 16s rRNA and S gene abundance. Results of empirical Bayesian kriging did not exhibit obvious patterns of microbial diversity in relation to weir proximity. Preliminary assessment of seasonal trends showed genes 16s rRNA and , soil N, and mean T-RF values to be greater in fall than in spring. Results highlight that weirs had no direct impact on microbial diversity or denitrification functional gene abundance. Correlations between microbial measures and environmental parameters suggest that adequate management of N runoff from agricultural landscapes will require ecological engineering beyond weirs to optimize N mitigation.

Effects of Subsurface Banding and Broadcast of Poultry Litter and Cover Crop on Soil Microbial Populations.

Agronomic management is aimed at managing the crop environment to maximize crop yield, but soil biology is often ignored. This study aimed to compare the application of poultry litter via broadcast and subsurface banding versus standard inorganic fertilizer to cotton ( L.) and their effects on soil bacterial populations and fecal indicator bacteria. The study comprised a randomized complete block design, with fertilizer and time of application as treatment effects and cover crop as a main effect. Soil cores were collected and analyzed from 2008 to 2014. Fecal indicator bacteria were at detection limits for all treatments, where the integron 1 gene was significantly elevated in litter plots. There were few differences between litter application approaches, but both significantly increased key biogeochemical genes over control plots, whereas a cover crop only increased soil moisture and urease C. Data suggested a positive residual effect of litter application with 16S, phosphatase A, and urease C genes elevated over controls, but similar to standard fertilizer plots. High-throughput 16S ribosomal RNA analysis suggested increased diversity and enrichment indices in litter and standard fertilizer over untreated control plots. Litter and standard fertilizer effects persisted 4 and 2 yr after application, respectively, as evidenced by residual library community structures. This study demonstrated the positive effects of litter application on the soil bacterial community when compared with untreated control plots. Some differences between standard fertilization and litter practices were noted and suggest that there is a positive residual effect on soil microbial populations associated with both practices.

Investigation of denitrifying microbial communities within an agricultural drainage system fitted with low-grade weirs.

Enhancing wetland characteristics in agricultural drainage ditches with the use of low-grade weirs, has been identified as a best management practice (BMP) to mitigate nutrient runoff from agriculture landscapes. A major objective of utilizing low-grade weirs as a BMP includes fostering environments suitable for the biogeochemical removal of nitrogen via denitrification. This study examined the spatial resolution of microbial communities involved in denitrification in agricultural drainage systems fitted with low-grade weirs. Appropriate sampling scales of microbial communities were investigated using 16S rRNA and denitrification functional genes nosZ, nirS, and nirK via quantitative polymerase chain reaction (qPCR) and terminal-restriction fragment length polymorphism (T-RFLP) analysis. Genes 16S rRNA, nosZ, and nirS were all successfully detected in soil samples, while nirK was below the detection limit throughout the study. Utilizing a combination of three sampling regimes (management, reach, catchment) was found to be effective in capturing microbial community patterns, as ANOVA results revealed nosZ gene abundance was significantly greater at the management rather than reach scale (p = 0.045; F = 3.311), although, no significant differences were observed in 16S rRNA or nirS between sampling scales (p > 0.05). A Pearson correlation matrix confirmed that 16S rRNA and nosZ gene abundances were positively correlated with soil carbon (C), nitrogen (N), and moisture, while nirS abundance was only positively correlated with soil C and soil moisture. This highlights the potential for wetland-like characteristics to be recovered in agricultural drainage systems, as weir proximity is observed to enhance soil moisture and conditions for N remediation. This study provides the basis for additional investigations of these unique environments in the Mississippi Alluvial Valley and a starting point for adaptive management to enhance agricultural drainage systems for microbial communities towards nutrient remediation goals.