Characterization of the reniform nematode genome by shotgun sequencing.

The reniform nematode (RN), a major agricultural pest particularly on cotton in the United States, is among the major plant-parasitic nematodes for which limited genomic information exists. In this study, over 380 Mb of sequence data were generated from pooled DNA of four adult female RNs and assembled into 67,317 contigs, including 25,904 (38.5%) predicted coding contigs and 41,413 (61.5%) noncoding contigs. Most of the characterized repeats were of low complexity (88.9%), and 0.9% of the contigs matched with 53.2% of GenBank ESTs. The most frequent Gene Ontology (GO) terms for molecular function and biological process were protein binding (32%) and embryonic development (20%). Further analysis showed that 741 (1.1%), 94 (0.1%), and 169 (0.25%) RN genomic contigs matched with 1328 (13.9%), 1480 (5.4%), and 1330 (7.4%) supercontigs of Meloidogyne incognita, Brugia malayi, and Pristionchus pacificus, respectively. Chromosome 5 of Caenorhabditis elegans had the highest number of hits to the RN contigs. Seven putative detoxification genes and three carbohydrate-active enzymes (CAZymes) involved in cell wall degradation were studied in more detail. Additionally, kinases, G protein-coupled receptors, and neuropeptides functioning in physiological, developmental, and regulatory processes were identified in the RN genome.

Nitrate reduction by commercially available nitrate reductases: bio-catalytic potentials and enzymatic activities in the presence of metals ions.

Commercially available nitrate reductases from corn, Aspergillus niger, and Escherichia coli have the potential to mitigate excess nitrate in soils and water sources. In this study, in vitro experiments were conducted to evaluate nitrate reduction by commercially available nitrate reductases from three major sources (plant, fungi and bacteria), their biocatalytic potentials and activities in the presence of varied concentrations of Cd(2+), Cu(2+), Ni(2+), Co(2+), Cr(6+), Fe(2+), Zn(2+), and Pb(2+). The results showed that the activity, V (max), and potential to reduce nitrate was in the order: corn > A. niger > E. coli. The kinetic constant (K (m)) based on the various substrates used demonstrated that the binding affinity was generally highest for E. coli and lowest for A. niger. Based on the specificity constants obtained in this study, nitrate reductase from corn was the most efficient of all the enzymes assayed, yet that from E. coli showed the least. Nitrate reductase from corn and A. niger showed more variations with increase in metal ions concentrations compared to E. coli (with the exception of Cu(2+)). Information reported in this study will enable the assessment of the contributions and sources of nitrate reductases in mitigating environmental and health issues resulting from nitrate pollution.

Pyrosequencing reveals bacteria carried in different wind-eroded sediments.

Little is known about the microbial communities carried in wind-eroded sediments from various soil types and land management systems. The novel technique of pyrosequencing promises to expand our understanding of the microbial diversity of soils and eroded sediments because it can sequence 10 to 100 times more DNA fragments than previous techniques, providing enhanced exploration into what microbes are being lost from soil due to wind erosion. Our study evaluated the bacterial diversity of two types of wind-eroded sediments collected from three different organic-rich soils in Michigan using a portable field wind tunnel. The wind-eroded sediments evaluated were a coarse sized fraction with 66% of particles >106 µm (coarse eroded sediment) and a finer eroded sediment with 72% of particles <106 µm. Our findings suggested that (i) bacteria carried in the coarser sediment and fine dust were effective fingerprints of the source soil, although their distribution may vary depending on the soil characteristics because certain bacteria may be more protected in soil surfaces than others; (ii) coarser wind-eroded sediment showed higher bacterial diversity than fine dust in two of the three soils evaluated; and (iii) certain bacteria were more predominant in fine dust (, , and ) than coarse sediment ( and ), revealing different locations and niches of bacteria in soil, which, depending on wind erosion processes, can have important implications on the soil sustainability and functioning. Infrared spectroscopy showed that wind erosion preferentially removes particular kinds of C from the soil that are lost via fine dust. Our study shows that eroded sediments remove the active labile organic soil particulates containing key microorganisms involved in soil biogeochemical processes, which can have a negative impact on the quality and functioning of the source soil.

Mercury speciation and effects on soil microbial activities.

To study Hg toxicity on soil microbes and their activities, it is necessary to understand its various forms in soils. The objectives of this study were to investigate Hg speciation in four soil types spiked with Hg (300 mg kg(-1) soil) and its effects on soil microbial respiration and enzymes (amidohydrolases and phosphatase) activities. An assessment of the chemical forms, amounts, reactions, and mobility of Hg in soils and sediments is of significant importance to improve and maintain soil and environmental health and sustainability. Mercury speciation analysis was investigated under acidic and alkaline conditions using a modified sequential procedure, which differentiates Hg into the four distinct fractions. Soil microbial respiration and enzymes activities were determined under laboratory settings, by incubating the soils at 25°C for 30 days, and then determining the amount of CO(2) evolved. Speciation results revealed that the water soluble form was the least, with < 1% of the total Hg in the soil types investigated irrespective of the pH condition, while the residual fraction was the most abundant (> 80%) in Canisteo, Houston, and Ketona soils under acidic conditions and < 35% in Decatur soil. Under alkaline conditions, the residual fraction was ≤ 70% in Canisteo, Houston, and ketona and ≤ 29% in Decatur soil. The exchangeable fraction was the second most abundant fraction in the soils used ranging from 3.7-50.0% under acid conditions and 16.9-52.1% under alkaline conditions indicating that Hg desorption was found to be more favorable under alkaline than acidic conditions. Soil respiration was suppressed by Hg especially at the 100 mg kg(-1) concentration level. Amidohydrolases and phosphatases' response in the presence of Hg was variable. Amidohydrolases were more sensitive to Hg (18-90%) than phosphatase (0-35%) in all soils. This study demonstrated that the forms in which Hg exist in soils may determine its bioavailability and toxicity. Also microbial respiration and enzyme activities are potential bioindicators of heavy metal contamination of the environment.

Proteomic Analysis of Soybean Roots under Aluminum Stress.

Toxic levels of aluminum (Al) in acid soils inhibit root growth and cause substantial reduction in yields of Al-sensitive crops. Aluminum-tolerant cultivars detoxify Al through multiple mechanisms that are currently not well understood at genetic and molecular levels. To enhance our understanding of the molecular mechanisms involved in soybean Al tolerance and toxicity, we conducted proteomic analysis of soybean roots under Al stress using a tandem combination of 2-D-DIGE, mass spectrometry, and bioinformatics tools and Al-tolerant (PI 416937) and Al-sensitive (Young) soybean genotypes at 6, 51 or 72 h of Al treatment. Comparison of the protein profile changes revealed that aluminum induced Al tolerance related proteins and enzymes in Al-tolerant PI 416937 but evoked proteins related to general stress response in Al-sensitive Young. Specifically, Al upregulated: malate dehydrogenase, enolase, malate oxidoreductase, and pyruvate dehydrogenase, in PI 416937 but not in Young. These enzymes contribute to increased synthesis of citrate, a key organic acid involved in Al detoxification. We postulate that simultaneous transgenic overexpression of several of these enzymes would be a robust genetic engineering strategy for developing Al-tolerant crops.

Mercury concentration and distribution in soils impacted by long-term applied broiler litter.

Mercury (Hg) is a non-essential element for plants and animals nutrition. Its presence in agricultural systems is of concern due to its high potential toxicity. Mercury is persistent in the environment and has been listed as a pollutant by several environmental organizations. This work focuses on Hg concentrations and distributions, trends, and relationships with some properties of soils that have received repeated broiler litter application and currently under pasture. Results revealed significant increase in Hg concentration from 41 to 105 microg kg(-1) and downward transport in the fields due to repeated applications. Correlation analysis indicated that sulfur and soil bulk density significantly (0.626*** and -0.645*** at p < or = 0.05, respectively) influenced its accumulation and distribution in this soil.

X-ray absorption near edge structure study of lead sorption on phosphate-treated kaolinite.

Presorbed phosphate significantly increases Pb sorption on the phyllosilicate kaolinite in the pH range from 4to 8. The sorbed Pb-to-P molar ratios over this pH range stray little from the molar ratio found in the mineral pyromorphite, suggesting sorbed phosphate reacts with soluble Pb to form a surface precipitate similar to pyromorphite. X-ray absorption near edge structure (XANES) studies at the Pb L3-edge support this interpretation. In particular, the fine structure of first-derivative Pb L3-edge XANES spectra of Pb species sorbed to phosphate-treated kaolinite samples covering a pH range extending from 4 to 10 match the fine structure of the spectrum of pyromorphite. Although the productis structurally and compositionally similarto pyromorphite, the ion activity product in the pH range 4-6 was undersaturated with respect to the solubility product of pyromorphite.

Tillage, cropping systems, and nitrogen fertilizer source effects on soil carbon sequestration and fractions.

Quantification of soil carbon (C) cycling as influenced by management practices is needed for C sequestration and soil quality improvement. We evaluated the 10-yr effects of tillage, cropping system, and N source on crop residue and soil C fractions at 0- to 20-cm depth in Decatur silt loam (clayey, kaolinitic, thermic, Typic Paleudults) in northern Alabama, USA. Treatments were incomplete factorial combinations of three tillage practices (no-till [NT], mulch till [MT], and conventional till [CT]), two cropping systems (cotton [Gossypium hirsutum L.]-cotton-corn [Zea mays L.] and rye [Secale cereale L.]/cotton-rye/cotton-corn), and two N fertilization sources and rates (0 and 100 kg N ha(-1) from NH(4)NO(3) and 100 and 200 kg N ha(-1) from poultry litter). Carbon fractions were soil organic C (SOC), particulate organic C (POC), microbial biomass C (MBC), and potential C mineralization (PCM). Crop residue varied among treatments and years and total residue from 1997 to 2005 was greater in rye/cotton-rye/cotton-corn than in cotton-cotton-corn and greater with NH(4)NO(3) than with poultry litter at 100 kg N ha(-1). The SOC content at 0 to 20 cm after 10 yr was greater with poultry litter than with NH(4)NO(3) in NT and CT, resulting in a C sequestration rate of 510 kg C ha(-1) yr(-1) with poultry litter compared with -120 to 147 kg C ha(-1) yr(-1) with NH(4)NO(3). Poultry litter also increased PCM and MBC compared with NH(4)NO(3). Cropping increased SOC, POC, and PCM compared with fallow in NT. Long-term poultry litter application or continuous cropping increased soil C storage and microbial biomass and activity compared with inorganic N fertilization or fallow, indicating that these management practices can sequester C, offset atmospheric CO(2) levels, and improve soil and environmental quality.