Evaluation of PCR-based quantification techniques to estimate the abundance of atrazine chlorohydrolase gene atzA in rhizosphere soils

There are many challenges in the accurate quantification of bacterial genes, such as the atrazine-degrading enzyme antA from Pseudomonas sp. strain ADP, from soil samples. We compared four quantitative methods for enumeration of atrazine-degrading bacteria in rhizosphere environments and utilized the optimal probe-based real-time polymerase chain reaction (PCR)-based method in an ongoing bioremediation experiment to monitor atzA copy number over time. We compared three quantitative PCR (qPCR) based methods--quantitative competitive PCR and two real-time qPCR methods--to traditional dilution-plate counting techniques. The optimal real-time qPCR assay was then used to monitor atzA copy number over time in the robust atrazine-degrading Pseudomonas sp. strain ADP-spiked rhizosphere environment. The use of sensitive and reliable probe-based real-time qPCRs for the enumeration of bacterial catabolic genes allows for their detection from soil samples and monitoring of potential degradative populations over time. The addition of arrazine-biodegrading bacteria into arrazine-contaminated sites to remove entrapped atrazine is a promising approach for mitigating atrazine pollution and its metabolites. The methodology contained herein will allow for optimal monitoring of atzA in rhizosphere soil with or without the addition of biodegradative Pseudomonas sp. strain ADP of bacteria.     

Sediment Contaminant Chemistry and Toxicity of Freshwater Urban Wetlands in Southern California1

Brown, Jeffrey S., Martha Sutula, Chris Stransky, John Rudolph, and Earl Byron, 2010. Sediment Contaminant Chemistry and Toxicity of Freshwater Urban Wetlands in Southern California. Journal of the American Water Resources Association (JAWRA) 46(2):367-384. DOI: 10.1111/j.1752-1688.2009.00407.x Abstract: Wetlands provide many critical functions in urban ecosystems, including habitat for wetland-dependent fauna and enhancement of water quality. Interest in restoring or creating wetlands to enhance these functions is increasing due to the scale and extent of wetland loss and water quality problems associated with urbanization. One of the most pressing questions associated with urban wetland restoration is the extent to which urban wetlands tend to concentrate contaminants, and if so, whether an associated risk to wildlife exists. The goal of this study was to better understand these potential risks, and the associated tradeoffs with using wetlands to treat urban runoff. Sediment toxicity, contaminant chemistry, and macroinvertebrate (MI) community metrics were measured in 21 southern California wetlands that receive urban runoff as their primary water source. MI organisms in 18 of the 21 urban wetlands examined were considered to be at risk due to sediment contaminant concentrations and toxicity. Most of the sites were either toxic to the amphipod Hyalella azteca, exceeded a sediment quality guideline, or both. Sediment chemistry and toxicity identification evaluation studies suggest that pyrethroid pesticides may have been responsible for much of the toxicity documented in this study. The mean Probable Effects Concentration quotient (an index of degree of sediment contamination) was found to negatively correlate with MI diversity in these wetlands suggesting that toxicity was affecting organisms at the base of the food chain in these wetlands.     

Bioremediation of atrazine-contaminated soil by forage grasses: transformation, uptake, and detoxification

A sound multi-species vegetation buffer design should incorporate the species that facilitate rapid degradation and sequestration of deposited herbicides in the buffer. A field lysimeter study with six different ground covers (bare ground, orchardgrass, tall fescue, timothy, smooth bromegrass, and switchgrass) was established to assess the bioremediation capacity of five forage species to enhance atrazine (ATR) dissipation in the environment via plant uptake and degradation and detoxification in the rhizosphere. Results suggested that the majority of the applied ATR remained in the soil and only a relatively small fraction of herbicide leached to leachates (<15%) or was taken up by plants (<4%). Biological degradation or chemical hydroxylation of soil ATR was enhanced by 20 to 45% in forage treatment compared with the control. Of the ATR residues remaining in soil, switchgrass degraded more than 80% to less toxic metabolites, with 47% of these residues converted to the less mobile hydroxylated metabolites 25 d after application. The strong correlation between the degradation of N-dealkylated ATR metabolites and the increased microbial biomass carbon in forage treatments suggested that enhanced biological degradation in the rhizosphere was facilitated by the forages. Hydroxylated ATR degradation products were the predominant ATR metabolites in the tissues of switchgrass and tall fescue. In contrast, the N-dealkylated metabolites were the major degradation products found in the other cool-season species. The difference in metabolite patterns between the warm- and cool-season species demonstrated their contrasting detoxification mechanisms, which also related to their tolerance to ATR exposure. Based on this study, switchgrass is recommended for use in riparian buffers designed to reduce ATR toxicity and mobility due to its high tolerance and strong degradation capacity.     

Dominance rank differences in the energy intake and expenditure of female Bwindi mountain gorillas

Socioecological models predict that contest competition for clumped foods can lead to higher energy intake and lower energy expenditure for higher-ranking individuals. Here, we examine the relationships between dominance rank and energy intake and expenditure of female mountain gorillas in Bwindi Impenetrable National Park, Uganda (Gorilla beringei beringei). Bwindi gorillas have weak dominance relationships, feed on nonreproductive plant parts throughout the year, and consume fruit when it is seasonally available. We used behavioral observations on one group of gorillas and nutritional analysis of their major food items to calculate energy intake rates and estimated energy expenditure. Using linear mixed models, we found a significant positive relationship between dominance rank and energy intake rates, due to higher-ranking females having faster ingestion rates, rather than consuming foods with higher energy concentrations. Lower-ranking females did not spend significantly more time feeding to compensate for their lower energy intake rates. Lower-ranking females spent significantly more time traveling than higher-ranking females, leading to a negative relationship between dominance rank and energy expenditure. The combined results revealed a significant positive relationship between dominance rank and energy balance. Higher-ranking females did not spend longer feeding on fruit than lower-ranking ones, and the relationship between dominance rank and energy intake rates was not stronger when fruit was available. According to socioecological models, these results suggest that contest competition may be occurring with both fruit and nonreproductive plant parts, which would be consistent with growing evidence that nonreproductive plant parts can be contestable.     

Analysis of individual year-classes of a marine fish reveals little evidence of first-generation hybrids between cryptic species in sympatric regions

As settled juveniles and adults, blue rockfish (Sebastes mystinus) are nonmigratory inhabitants of kelp and rocky reef habitats along the California coast, USA, and prior to settlement, they possess a pelagic larval and juvenile stage lasting 3–5 months. A previous study of adults revealed two cryptic species within S. mystinus and evidence of reproductive isolation in a region where both cryptic adults co-occur. Given this pattern of reproductive isolation, we investigated the degree of hybridization or introgression in individual year-classes shortly after juvenile settlement in two different years (2001 and 2002). Using microsatellite markers, we found little indication of hybridization in new juvenile year-classes despite an adult population that comprised both cryptic species. However, we found an average of two percent of hybrid or introgressed individuals in regions with a low frequency of one of the two species. Therefore, while the lack of hybrids or introgression supports the hypothesis of reproductive isolation between the cryptic species within S. mystinus, the age-structured analysis also revealed a spatial pattern of low-frequency differences in the number of introgressed individuals. These results suggest that reproductive barriers may breakdown when one of the two species predominates the regional adult gene pool.     

Invasive competitor and native seed predators contribute to rarity of the narrow endemic Astragalus sinuatus Piper

The conservation of rare plant species hinges on our ability to identify the underlying mechanisms that limit rare plant populations. Theory on rarity suggests that both predispersal seed predation and competition can be important mechanisms influencing abundance and/or distribution of rare plant populations. Yet few studies have tested these interactions, and those that have evaluated each mechanism independently. Astragalus sinuatus Piper (Whited's milkvetch) is a narrow endemic plant species restricted to eight populations within a 10-km2 area in eastern Washington. We used experimental and observational methods to test the effects of native insect predispersal seed predators and an invasive grass (Bromus tectorum L. [cheatgrass]) on seed set and population density of A. sinuatus. We quantified per capita seed production and pod predation rates across four sites and among four years. Seed predation rates were high across four sites (66-82%) and all years (65-82%). Experimental reduction of predispersal seed predators significantly increased per capita seed set of A. sinuatus (164-345%) at two experimental sites. Concurrently, two seed addition experiments demonstrated the effect of seed loss and presence of B. tectorum on seedling recruitment and establishment of A. sinuatus over four growing seasons. In the first seed addition experiment, we found no difference in recruitment and establishment between low (40) and high (120) seed addition levels. In the second addition experiment (one level of addition; 40 seeds), we found that recruitment and survivorship increased 200% in plots where B. tectorum was removed compared to plots where B. tectorum was present. Thus, seed addition had no impact in the presence of B. tectorum; conversely, in the absence of B. tectorum, seed addition was highly effective at increasing population numbers. Results suggest that, in areas where B. tectorum is present, recruitment is site limited, and it is seed limited when B. tectorum is absent. We recommend that managers reduce B. tectorum in an effort to increase population growth of A. sinuatus; in areas where B. tectorum is absent, short-term reduction of insect predators should be considered as a strategy to increase population growth of this rare species.     

Migration of As, Hg, Pb, and Zn in arroyo sediments from a semiarid coastal system influenced by the abandoned gold mining district at El Triunfo, Baja California Sur, Mexico

Extensive waste deposits (tailings) and ash from the ignition oven of the abandoned gold mine of mining district El Triunfo (MD-ET) in Baja California Sur, Mexico have released trace elements into the sediments of the Hondo-Las Gallinas-El Carrizal arroyo, which connects to the Pacific Ocean through an evaporitic basin. Migration of these elements through the arroyo is mainly caused by winds or tropical hurricanes that occur sporadically during the summer and cause the otherwise dry arroyo to overflow. To evaluate the concentration and distribution of the elements As, Hg, Pb, and Zn along the 48 km arroyo, surface sediments were collected from 26 sites, ranging from close to the MD-ET to the mouth of the arroyo at the Pacific Ocean. Concentrations in tailings and ash were for As 8890 and 505?000 mg kg(-1); for Hg 0.336 and 54.9 mg kg(-1); for Pb 92,700 and 19,300 mg kg(-1); and for Zn 49,600 and 1380 mg kg(-1). The average of the Normalized Enrichment Factor (Av-NEF) in surface sediments, calculated using background levels, indicates that the sediments are severely contaminated with As and Zn (Av-NEF = 22), Pb (Av-NEF = 24) and with a moderate contamination of Hg (Av-NEF = 7.5). The anthropogenic influence of those elements is reflected in the arroyo sediments as far as 18 km away from the MD-ET, whereas the samples closest to the discharge into the Pacific Ocean show a natural to moderate enrichment for As and Zn and low or no enrichment for Hg and Pb. A principal components analysis identified four principal components that explained 90% of the total variance. Factor 1 was characterized by a high positive contribution of the anthropogenic source elements, especially As, Pb, and Zn (37%), whereas Factor 2 was strongly correlated with the oxy-hydroxides of Fe and Mn (27%). Factor 3 was correlated with Li (16%) and Factor 4 with Al (10%), which indicates more than one source of lithogenic composition, though they played a minor role in the distribution of the elements.     

Reducing herbicides and veterinary antibiotics losses from agroecosystems using vegetative buffers

Multiple species vegetative buffer strips (VBSs) have been recommended as a cost-effective approach to mitigate agrochemical transport in surface runoff derived from agronomic operations, while at the same time offering a broader range of long-term ecological and environmental benefits. However, the effect of VBS designs and species composition on reducing herbicide and veterinary antibiotic transport has not been well documented. An experiment consisting of three VBS designs and one continuous cultivated fallow control replicated in triplicate was conducted to assess effectiveness in reducing herbicide and antibiotic transport for claypan soils. The three VBS designs include (i) tall fescue, (ii) tall fescue with a switchgrass hedge barrier, and (iii) native vegetation (largely eastern gamagrass). Rainfall simulation was used to create uniform antecedent soil moisture content in the plots and to generate runoff. Our results suggested that all VBS significantly reduced the transport of dissolved and sediment-bound atrazine, metolachlor, and glyphosate in surface runoff by 58 to 72%. Four to 8 m of any tested VBS reduced dissolved sulfamethazine transport in the surface runoff by more than 70%. The tall fescue VBS was overall most effective at reducing dissolved tylosin and enrofloxacin transport in the runoff (>75%). The developed exponential regression models can be used to predict expected field-scale results and provide design criteria for effective field implementation of grass buffers. Our study has demonstrated that an optimized VBS design may achieve desired agrochemical reductions and minimize acreage removed from crop production.     

Herbicide Transport in Goodwater Creek Experimental Watershed: II. Long‐Term Research on Acetochlor,Alachlor, Metolachlor,and Metribuzin1

Lerch, R.N., E.J. Sadler, C. Baffaut, N.R. Kitchen, and K.A. Sudduth, 2010. Herbicide Transport in Goodwater Creek Experimental Watershed: II. Long‐Term Research on Acetochlor, Alachlor, Metolachlor, and Metribuzin. Journal of the American Water Resources Association (JAWRA) 1‐15. DOI: 10.1111/j.1752‐1688.2010.00504.x Abstract: Farmers in the Midwestern United States continue to be reliant on soil‐applied herbicides for weed control in crop production, and herbicide contamination of streams remains an environmental problem. The main objective of this study was to analyze trends in concentration and load of acetochlor, alachlor, metolachlor, and metribuzin in Goodwater Creek Experimental Watershed (GCEW) from 1992 to 2006. A secondary objective was to document the effects of best management practices (BMPs) implemented within GCEW on herbicide transport trends. Median relative herbicide loads, as a percent of applied, were 3.7% for metolachlor, 1.3% for metribuzin, 0.36% for acetochlor, and 0.18% for alachlor. The major decrease in alachlor use and increase in acetochlor use caused shifts in flow‐weighted concentrations that were observed over the entire concentration range. The smaller decrease in metolachlor use led to a consistent decreasing time trend only for the upper end of the concentration distribution. Metribuzin also showed moderate decreases in concentration with time since 1998. Annual loads were generally correlated to second quarter discharge. Despite extensive education efforts in the watershed, conservation BMPs within GCEW were mainly implemented to control erosion, and therefore had no discernable impact on reducing herbicide transport. Overall, changes in herbicide use and second quarter discharge had the greatest effect on trends in flow‐weighted concentration and annual load.