Net primary production in three bioenergy crop systems following land conversion

Aims Identifying the amount of production and the partitioning to above- and belowground biomass is generally the first step toward selecting bioenergy systems. There are very few existing studies on the dynamics of production following land conversion. The objectives of this study were to (i) determine the differences in aboveground net primary production (ANPP), belowground net primary production (BNPP), shoot-to-root ratio (S:R) and leaf area index in three bioenergy crop systems and (ii) evaluate the production of these three systems in two different land use conversions.Methods This investigation included biometric analysis of NPP on three agricultural sites converted from conservation reserve program (CRP) management to bioenergy crop production (corn, switchgrass and prairie mix) and three sites converted from traditional agriculture production to bioenergy crop production.Important findings The site converted from conventional agriculture produced smaller ANPP in corn (19.03±1.90 standard error [SE] Mg ha^-1 year^-1) than the site converted from CRP to corn (24.54±1.43 SE Mg ha^-1 year^-1). The two land conversions were similar in terms of ANPP for switchgrass (4.88±0.43 SE for CRP and 2.04±0.23 SE Mg ha^-1 year^-1 for agriculture) and ANPP for prairie mix (4.70±0.50 SE for CRP and 3.38±0.33 SE Mg ha^-1 year^-1 for agriculture). The BNPP at the end of the growing season in all the bioenergy crop systems was not significantly different (P = 0.75, N = 8).     

Responses of Second-Instar Male Nymphs of Four Mealybug Species (Hemiptera: Pseudococcidae) to Conspecific and Heterospecific Female Sex Pheromones

The response of the late second-instar male nymphs of the mealybug species (Hemiptera, Pseudococcidae), Planococcus citri (Risso), Planococcus ficus (Signoret), Pseudococcus cryptus Hempel Nipaecoccus viridis (Newstead), to their conspecific and heterospecific female pheromone was studied. Males that exhibited the typical appearance of late-second-instar nymphs were tested. The male behavior was monitored soon after their exposure to the tested female sex pheromone in glass Petri dish arenas. Male nymph behavior toward the pheromone source was characterized based on their aggregation on the disks in the arena. Males of all four tested mealybug species were attracted to their conspecific female pheromone. By contrast, almost no interceptions of male nymphs with disks impregnated with a heterospecific female pheromone were observed. The mode of attraction of each of male nymphs of P. ficus, among most of the tested individuals (>80%), to the conspecific female sex pheromone, (S)-lavandulyl senecioate and or (S)-lavandulyl isovalerate, was the same as the mode of attraction latter on as adult. We suggest that by being attracted to the conspecific pheromone these males may direct themselves to a suitable pupation site near conspecific non-sibling mature females, thus preventing inbreeding. The repellency of heterospecific sex pheromone to males that are looking for a pupation site suggests that the latter try to avoid close contact with heterospecific females.     

Genomic analysis of polycarpellary rice (Oryza sativa L.) through whole genome resequencing

There is a natural floral organ mutant of rice (var. Jugal) where the florets, popularly known as spikelet bear multiple carpels and produce multiple kernels in most of its grain. In our earlier work a detailed study has been done on its morpho-anatomical structure with allelic diversity and expression study of the major genetic loci associated with floral organ development. In present study high throughput whole genome sequencing was done which generated about of 3.7 million base pair genomic data for downstream analysis. The reads were about 101 bases long and mapped to the Oryza sativa var. Nipponbare as reference genome. Genome wide variant analysis detected 1,096,419 variants which included 943,033 SNPs and 153,386 InDels. A total of 24,920 non-synonymous SNPs were identified for 11,529 identified genes. Chromosome-wise distribution of uniquely mapped reads onto reference genome showed that maximum reads were mapped to 1st chromosome and least to 9th chromosome. 10th chromosome showed highest density of variations (about 325.6 per 100 kb genome sequence). Detailed sequence analysis of 23 floral organ developmental genes detected 419 potent variants where DL (Drooping Leaf) and OSH1 (Oryza sativa Homeobox1) genes showed highest number (32) of variants; whereas, MADS21 (Minichromosome Agamous Deficient Serum Factor 21) gene have lowest number (5) of variants. The information generated in this study will enrich the genomics of floral organ development in indica rice and cereal crops in general.

     

Denitrifying bacteria from the genus Rhodanobacter dominate bacterial communities in the highly contaminated subsurface of a nuclear legacy waste site

The effect of long-term mixed-waste contamination, particularly uranium and nitrate, on the microbial community in the terrestrial subsurface was investigated at the field scale at the Oak Ridge Integrated Field Research Challenge (ORIFRC) site in Oak Ridge, TN. The abundance, community composition, and distribution of groundwater microorganisms were examined across the site during two seasonal sampling events. At representative locations, subsurface sediment was also examined from two boreholes, one sampled from the most heavily contaminated area of the site and another from an area with low contamination. A suite of DNA- and RNA-based molecular tools were employed for community characterization, including quantitative PCR of rRNA and nitrite reductase genes, community composition fingerprinting analysis, and high-throughput pyrotag sequencing of rRNA genes. The results demonstrate that pH is a major driver of the subsurface microbial community structure and that denitrifying bacteria from the genus Rhodanobacter (class Gammaproteobacteria) dominate at low pH. The relative abundance of bacteria from this genus was positively correlated with lower-pH conditions, and these bacteria were abundant and active in the most highly contaminated areas. Other factors, such as the concentration of nitrogen species, oxygen level, and sampling season, did not appear to strongly influence the distribution of Rhodanobacter bacteria. The results indicate that these organisms are acid-tolerant denitrifiers, well suited to the acidic, nitrate-rich subsurface conditions, and pH is confirmed as a dominant driver of bacterial community structure in this contaminated subsurface environment.     

Environmental enteropathy: critical implications of a poorly understood condition

Environmental enteropathy (also called tropical enteropathy) is a subclinical condition caused by constant fecal-oral contamination and resulting in blunting of intestinal villi and intestinal inflammation. Although these histological changes were discovered decades ago, the clinical impact of environmental enteropathy is just starting to be recognized. The failure of nutritional interventions and oral vaccines in the developing world may be attributed to environmental enteropathy, as the intestinal absorptive and immunologic functions are significantly deranged. Here we review the existing literature and examine potential mechanisms of pathogenesis for this poorly understood condition.     

Diversity of nifH Genotypes in Floating Periphyton Mats Along a Nutrient Gradient in the Florida Everglades

Periphyton mats are an important component of many wetland ecosystems, performing a range of vital ecosystem functions, including nitrogen fixation. The composition and integrity of these mats are affected by nutrient additions, which might result in changes in their function. The overall objective of this study was to investigate the distribution of nifH sequences in floating periphyton mats collected along a nutrient gradient in the Florida Everglades. Distribution of nifH clone libraries indicated nutrient enrichment selected primarily for sequences branching deeply within the heterocystous cyanobacteria and within a novel group of cyanobacteria; sequences from low-nutrient sites were broadly distributed, with no clear dominance of sequences associated with heterocystous and nonheterocystous cyanobacteria and alpha-, gamma-, and delta-proteobacteria. The dominance of heterocystous cyanobacteria in nutrient-enriched sites and the lack of clear dominance by heterocystous cyanobacteria is consistent with previously reported diurnal cycles of nitrogen fixation rates in these systems. Sequences clustering with those harbored by methanotrophs were also identified; sequences from nutrient-impacted and transition regions clustered with those characteristic of type II methanotrophs, and sequences from oligotrophic regions clustered with type I methanotrophs.     

An immuno-marking technique for thrips

Rabbit immunoglobulin G (R‐IgG) was used successfully as an external mark for thrips. Females of both Thrips tabaci Lindeman and Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae) were marked with 1 mg ml^?1 R‐IgG solution with 1%‘Tween 20’ by the contact exposure method. Determining the retention of the mark was by running the rinsing solution of individual thrips in an enzyme‐linked immunosorbent assay (ELISA). The sandwich ELISA method was used with an additional biotin–avidin step. The threshold for a positive marking score was defined as three times the mean optical density readings of the negative control thrips. Under laboratory conditions, on bean pods, all marked thrips scored positive up to 6 days after marking (DAM). When marked thrips were kept in the laboratory on marigold flowers for 2 days, they all scored positive. When marked and unmarked thrips were placed together on these flowers, the mark was transferred to 10–20% of the unmarked thrips and they became positive. Under field conditions, on sticky traps covered with water‐base glue, 100, 80, and 20% of the marked T. tabaci scored positive by the 3rd, 6th, and 9th DAM, respectively. Under the same conditions 100, 90, and 10% of the marked F. occidentalis scored positive by the 3rd, 6th, and 9th DAM, respectively. The retention of the R‐IgG decreased significantly under conditions of wetness and high humidity. After 6 days on chive plants kept at 80–100% r.h., all marked thrips scored negative while on plants kept at 40–60% r.h., 85% of the marked thrips scored positive. Rabbit IgG can be used as an external marker for thrips. The suitability of this marking method for dispersal studies of these important pests needs to be evaluated.     

Microbial and Geochemical Assessment of Bauxitic Un-mined and Post-mined Chronosequence Soils from Mocho Mountains, Jamaica

Microorganisms are very sensitive to environmental change and can be used to gauge anthropogenic impacts and even predict restoration success of degraded environments. Here, we report assessment of bauxite mining activities on soil biogeochemistry and microbial community structure using un-mined and three post-mined sites in Jamaica. The post-mined soils represent a chronosequence, undergoing restoration since 1987, 1997, and 2007. Soils were collected during dry and wet seasons and analyzed for pH, organic matter (OM), total carbon (TC), nitrogen (TN), and phosphorus. The microbial community structure was assessed through quantitative PCR and massively parallel bacterial ribosomal RNA (rRNA) gene sequencing. Edaphic factors and microbial community composition were analyzed using multivariate statistical approaches and revealed a significant, negative impact of mining on soil that persisted even after greater than 20?years of restoration. Seasonal fluctuations contributed to variation in measured soil properties and community composition, but they were minor in comparison to long-term effects of mining. In both seasons, post-mined soils were higher in pH but OM, TC, and TN decreased. Bacterial rRNA gene analyses demonstrated a general decrease in diversity in post-mined soils and up to a 3-log decrease in rRNA gene abundance. Community composition analyses demonstrated that bacteria from the Proteobacteria (α, β, γ, δ), Acidobacteria, and Firmicutes were abundant in all soils. The abundance of Firmicutes was elevated in newer post-mined soils relative to the un-mined soil, and this contrasted a decrease, relative to un-mined soils, in proteobacterial and acidobacterial rRNA gene abundances. Our study indicates long-lasting impacts of mining activities to soil biogeochemical and microbial properties with impending loss in soil productivity.     

Influence of soil temperature, rainfall, and planting and harvest dates on Chaetocnema confinis (Coleoptera: Chrysomelidae) damage to sweetpotato roots

A study was carried out in 10 counties of North Carolina from 2004 to 2006 to determine the effect of planting and harvest times on flea beetle, Chaetocnema confinis Crotch (Coleoptera: Chrysomelidae), damage to sweetpotato, Ipomoea batatas (L.), storage roots. Planting and harvesting of sweetpotatoes later in the season resulted in less damage than early planting and harvesting. Regression analysis was done to study the relationship of weather parameters with the flea beetle damage. Weather parameters included air temperature (Celsius), soil temperature at 5- and 10-cm depth (Celsius), rainfall (millimeters), and soil moisture (volume:volume) at 0-10-, 10-40-, and 40-100-cm depth. The best regression model included mean soil temperature at 10-cm depth, total rainfall, and number of adults caught on yellow sticky traps as independent variables (all between 1 August and harvest date of each field). Soil temperature and adult catches on yellow sticky traps of C. confinis were positively related to damage, whereas rainfall was negatively correlated. The model explained 45% of the total variation in the flea beetle damage. Soil temperature alone accounted for 32% of the total variation in flea beetle damage followed by rainfall (9%) and adult catches (4%). When the time interval was limited to 30 d before harvest, soil temperature was still the best explanatory variable accounting for 23% of the total variation in flea beetle damage followed by rainfall (7%) and adult catches (4%). Understanding the effects of planting/harvesting and weather factors on flea beetle damage will be useful in predicting the time when the sweetpotato crop is at greater risk from high levels of damage by C. confinis.