Isolation of soil bacteria adapted to degrade humic acid-sorbed phenanthrene

The goal of these studies was to determine how sorption by humic acids affected the bioavailability of polynuclear aromatic hydrocarbons (PAHs) to PAH-degrading microbes. Micellar solutions of humic acid were used as sorbents, and phenanthrene was used as a model PAH. Enrichments from PAH-contaminated soils established with nonsorbed phenanthrene yielded a total of 25 different isolates representing a diversity of bacterial phylotypes. In contrast, only three strains of Burkholderia spp. and one strain each of Delftia sp. and Sphingomonas sp. were isolated from enrichments with humic acid-sorbed phenanthrene (HASP). Using [14C]phenanthrene as a radiotracer, we verified that only HASP isolates were capable of mineralizing HASP, a phenotype hence termed "competence." Competence was an all-or-nothing phenotype: noncompetent strains showed no detectable phenanthrene mineralization in HASP cultures, but levels of phenanthrene mineralization effected by competent strains in HASP and NSP cultures were not significantly different. Levels and rates of phenanthrene mineralization exceeded those predicted to be supported solely by the metabolism of phenanthrene in the aqueous phase of HASP cultures. Thus, competent strains were able to directly access phenanthrene sorbed by the humic acids and did not rely on desorption for substrate uptake. To the best of our knowledge, this is the first report of (i) a selective interaction between aerobic bacteria and humic acid molecules and (ii) differential bioavailability to bacteria of PAHs sorbed to a natural biogeopolymer.     

Effect of soil potassium availability on soybean aphid (Hemiptera: Aphididae) population dynamics and soybean yield

Studies were conducted to examine the effect of potassium (K) on soybean aphid, Aphis glycines Matsumura, population growth. A laboratory feeding assay examined the effect of K-deficient foliage on life table parameters of soybean aphids, and field experiments were designed to determine the effect of three soil K treatment levels on aphid populations and their impact on soybean yields. The feeding assay found that life table parameters differed between aphids feeding on the K-deficient and nondeficient soybean leaves. Soybean aphids in the K-deficient treatment exhibited significantly greater intrinsic rate of increase (r(m)), finite rate of increase (lambda), and net reproductive rate (Ro) relative to aphids feeding on nondeficient leaves. No significant difference was observed in mean generation time (T) between the two treatments. However, the field experiment repeated over 2 yr showed no effect of K on soybean aphid populations. Soybean aphid populations were high in unsprayed plots and feeding resulted in significant yield losses in 2002 at all three K treatment levels: when averaged across 2001 and 2002, unsprayed treatments yielded 22, 18, and 19.5% less than the sprayed plots in the low, medium, and high K treatments, respectively. No significant interaction was observed between aphid abundance and K level on soybean yields in either year. This study therefore suggests that although aphids can perform better on K-deficient plants, aphid abundance in the field may be dependent on additional factors, such as dispersal, that may affect final densities within plots.     

Mapping QTLs for root morphology of a rice population adapted to rainfed lowland conditions

In the rainfed lowlands, rice ( Oryza sativa L.) develops roots under anaerobic soil conditions with ponded water, prior to exposure to water stress and aerobic soil conditions that arise later in the season. Constitutive root system development in anaerobic soil conditions has been reported to have a positive effect on subsequent expression of adaptive root traits and water extraction during progressive water stress in aerobic soil conditions. We examined quantitative trait loci (QTLs) for constitutive root morphology traits using a mapping population derived from a cross between two rice lines which were well-adapted to rainfed lowland conditions. The effects of phenotyping environment and genetic background on QTLs identification were examined by comparing the experimental data with published results from four other populations. One hundred and eighty-four recombinant inbred lines (RILs) from a lowland indica cross (IR58821/IR52561) were grown under anaerobic conditions in two experiments. Seven traits, categorized into three groups (shoot biomass, deep root morphology, root thickness) were measured during the tillering stage. Though parental lines showed consistent differences in shoot biomass and root morphology traits across the two seasons, genotype-by-environment interaction (GxE) and QTL-by-environment interaction were significant among the progeny. Two, twelve, and eight QTLs for shoot biomass, deep root morphology, and root thickness, respectively, were identified, with LOD scores ranging from 2.0 to 12.8. Phenotypic variation explained by a single QTL ranged from 6% to 30%. Only two QTLs for deep root morphology, in RG256-RG151 in chromosome 2 and in PC75M3-PC11M4 in chromosome 4, were identified in both experiments. Comparison of positions of QTLs across five mapping populations (the current population plus populations from four other studies) revealed that these two QTLs for deep root morphology were only identified in populations that were phenotyped under anaerobic conditions. Fourteen and nine chromosome regions overlapped across different populations as putative QTLs for deep root morphology and root thickness, respectively. PC41M2-PC173M5 in chromosome 2 was identified as an interval that had QTLs for deep root morphology in four mapping populations. The PC75M3-PC11M4 interval in chromosome 4 was identified as a QTL for root thickness in three mapping populations with phenotypic variation explained by a single QTL consistently as large as 20-30%. Three QTLs for deep root morphology were found only in japonica/indica populations but not in IR58821/IR52561. The results identifying chromosome regions that had putative QTLs for deep root morphology and root thickness over different mapping populations indicate potential for marker-assisted selection for these traits.     

Soil H2-uptake in relation to soil properties and rhizobial H2-production

Summary The biological nature of soil H₂-consumption has been investigated. Soil microorganisms were capable to remove H₂ present in the gas phase at concentrations in the range of 200 ppm at rates varying between 0.2 and 1.0 l.min^–1. 100 g^–1. Free soil enzymes did not contribute significantly at the H₂ concentrations tested. Oxygen seemed to be the predominant electron acceptor. The influence of microbiological and physical soil properties on the H₂-uptake activity was examined for 38 soils.A highly significant correlation between biomass-C and H₂-uptake rate of the soil was noted, suggesting that the latter parameter might be useful as an indirect estimation of soil microbial biomass. The correlation was however not applicable for soils recently grown with legumes. Indeed, soya plants nodulated with aRhizobium strain with a weak hydrogen uptake capability, strongly increased the hydrogen oxidizing capability of the surrounding soil.     

A soybean mapping population specific to the early soybean production system.

The objective of this research was to create a soybean [Glycine max (L.) Merr] genetic resource in the form of a publicly available, well-characterized mapping population specific to maturity groups (MG) used in the early soybean production system. A total of 568 simple sequence repeat (SSR) markers were tested for polymorphism between soybean breeding line DS97-84-1 (MG IV) and germplasm line DT97-4290 (MG IV). A 90-genotype subset of an F2 population from a cross between these lines was evaluated for genetic linkage using 162 polymorphic SSRs, plant height, pod color (L2/l2), flower color (W1/w1) and stem termination (Dt1/dt1). A 1514 cM (Kosambi) genetic map covering 65% of the soybean genome based on 157 linked SSR markers was created. Comparison with the composite soybean genetic map was used to verify map order. Loci for pod color, flower color and stem termination fell in the expected position on the map indicating this is a normally segregating mapping population. Loci for height were identified on linkage groups C2, D1a, D1b, H, L, M and O. MG IV and V soybean genotypes are critical for the early soybean production system widely used in the midsouthern US. However, only two mapping populations have been reported in Soybase for MG IV and V genotypes. Additionally, the parents used in this cross are known to differ in their response to soybean cyst nematode and charcoal rot, which constitute two major pathology threats to Midsouth soybean production. The population and map reported herein represent an important genetic resource for the early soybean production system.     

Evaluation of soybean RFLP marker diversity in adapted germ plasm

Summary Soybean RFLP markers have been primarily developed and genetically mapped using wide crosses between exotic and adapted genotypes. We have screened 38 soybean lines at 128 RFLP marker loci primarily to characterize germ plasm structure but also to evaluate the utility of RFLP markers identified in unadapted populations. Of these DNA probes 70% detected RFLPs in this set of soybean lines with an average polymorphism index of 0.30. This means that only 1 out of 5 marker loci was informative between any particular pair of adapted soybean lines. The variance associated with the estimation of RFLP genetic distance (GD_R) was determined, and the value obtained suggested that the use of more than 65–90 marker loci for germ plasm surveys will add little precision. Cluster analysis and principal coordinate analysis of the GD_R matrix revealed the relative lack of diversity in adapted germ plasm. Within the cultivated lines, several lines adapted to Southern US maturity zones also appeared as a separate group. GD_R data was compared to the genetic distance estimates obtained from pedigree analysis (GD_P). These two measures were correlated with r = 0.54 for all 38 lines, but the correlation increased to r = 0.73 when only adapted lines were analyzed.     

Seed quality QTL in a prominent soybean population

Soybean [Glycine max (L.) Merr.] is a versatile crop due to its multitude of uses as a high protein meal and vegetable oil. Soybean seed traits such as seed protein and oil concentration and seed size are important quantitative traits. The objective of this study was to identify representative protein, oil, and seed size quantitative trait loci (QTL) in soybean. A recombinant inbred line (RIL) population consisting of 131 F₆-derived lines was created from two prominent ancestors of North American soybeans (Essex and Williams) and the RILs were grown in six environments. One hundred simple sequence repeat (SSR) markers spaced throughout the genome were mapped in this population. There were a total of four protein, six oil, and seven seed size QTL found in this population. The QTL found in this study may assist breeders in marker-assisted selection (MAS) to retain current positive QTL in modern soybeans while simultaneously pyramiding additional QTL from new germplasm.     

Diversity within a population of Shigella sonnei according to markers of medicinal preparations

As revealed in this study, S. sonnei population is represented by two clusters with respect to the sensitivity to different antibiotics. A higher degree of diversity was observed with respect to the action of streptomycin, kefzol, ampicillin, chloramphenicol and kanamycin in comparison with the action of gentamicin, nevigramon, rafampicin, tetracycline and polymyxin. The level of diversity of S. sonnei with respect to the sensitivity to antibiotics under study underwent essential changes during the calendar year. The distributions obtained study quite closely corresponded to changes in Sonne dysentery morbidity observed within the year period: the first cluster corresponded to the period of morbidity between the seasons and the second one, to the seasonal period of morbidity. The minimal coefficient of diversity fell on May while the maximum--on September. The minimal level of S. sonnei diversity, as a rule, corresponds to the minimum biosystems stability.     

Ensifer shofinae sp. nov., a novel rhizobial species isolated from root nodules of soybean (Glycine max)

Two bacterial strains isolated from root nodules of soybean were characterized phylogenetically as members of a distinct group in the genus Ensifer based on 16S rRNA gene comparisons. They were also verified as a separated group by the concatenated sequence analyses of recA, atpD and glnII (with similarities ≤93.9% to the type strains for defined species), and by the average nucleotide identities (ANI) between the whole genome sequence of the representative strain CCBAU 251167^T and those of the closely related strains in Ensifer glycinis and Ensifer fredii (90.5% and 90.3%, respectively). Phylogeny of symbiotic genes (nodC and nifH) grouped these two strains together with some soybean-nodulating strains of E. fredii, E. glycinis and Ensifer sojae. Nodulation tests indicated that the representative strain CCBAU 251167^T could form root nodules with capability of nitrogen fixing on its host plant and Glycine soja, Cajanus cajan, Vigna unguiculata, Phaseolus vulgaris and Astragalus membranaceus, and it formed ineffective nodules on Leucaena leucocephala. Strain CCBAU 251167^T contained fatty acids 18:1 ω9c, 18:0 iso and 20:0, differing from other related strains. Utilization of l-threonine and d-serine as carbon source, growth at pH 6.0 and intolerance of 1% (w/v) NaCl distinguished strain CCBAU 251167^T from other type strains of the related species. The genome size of CCBAU 251167^T was 6.2 Mbp, comprising 7,581 predicted genes with DNA G+C content of 59.9 mol% and 970 unique genes. Therefore, a novel species, Ensifer shofinae sp. nov., is proposed, with CCBAU 251167^T (=ACCC 19939^T = LMG 29645^T) as type strain.     

White lupin utilizes soil phosphorus that is unavailable to soybean

White lupin (Lupinus albus L. var. Ultra) and soybean (Glycine max L. var. Elgin) were grown in an acidic soil low an available phosphorus (P) to investigate their different capacities to acquire soil phosphorus. Experiments done in the controlled environment of a biotron were supplemented with four separate greenhouse experiments. Lupin and soybean were grown in monoculture and intercropped on a soil with low available P that was labeled with carrier-free ³²P as phosphate. Lupin had significantly lower values of specific activity of ³²P and higher values of isotopically exchangeable P than soybean in all cases. The results show that lupin utilizes soil P from a normally non-labile pool of soil P that is not utilized by soybean.     

Differential response of soybean genotypes to soil pH and manganese application

An experiment was conducted at Tamil Nadu Agricultural University, Coimbatore, India during 1982 wet season (June–July) to study the root activity and rooting pattern of IR-20 rice as influenced by urea insecticide combinations by a³²P absorption technique. The treatments involved a factorial combination of four levels of N (0, 60, 90 and 120 kg N/ha) as urea and three levels of insecticides (no insecticide, carbofuran @ 0.75 kg a.i./ha and phorate @ 1.0 kg a.i./ha). The root activity measured in terms of the amount of³²P absorbed by the plant, increased considerably by the application of urea and insecticides (carbofuran or phorate) as well as due to their interactions. The root activity increased upto 120 kg N ha⁻¹. Carbofuran or phorate application increased root activity and the effect of carbofuran was greater than that of phorate. Nitrogen-insecticide interaction was positive on root activity upto 120 kg N ha⁻¹ and the effect was more marked with carbofuran and N combinations. But the percentage distribution of active roots of rice could not be influenced by levels of N, insecticides or their interactions. About 80 percent of the roots of IR 20 rice forage within 10 cm from the surface. The enhanced root activity due to application of N and insecticides (carbofuran and phorate) increased the uptake of major and micro-nutrients. the phytotonic effects of carbofuran and phorate on rice works by triggering the root activity of the crop.     

Variations of soil structure and microbial population in a compost amended soil

Changes in soil structure and in microbial population were recorded in a long term field experiment over the growing season of maize (June–November). Determinations were made on samples from plots which had received, for two years, the following treatments: mineral fertilizers, farmyard manure and three rates of compost. Seasonal variations were observed for the stability of soil aggregates, total porosity, pore size distribution, mycorrhizal infection and aerobic cellulolytic microorganisms. The stability of the soil aggregates changed in a similar way to that found for both mycorrhizal infection and the number of aerobic cellulolytic microorganisms. Physical characteristics were not affected in any instance by the organic dressings and microbiological populations were generally influenced only by the higher doses of compost.     

Estimating the heritability of female lifetime fecundity in a locally adapted Drosophila melanogaster population

The heritability of genome‐wide fitness that is expected in finite populations is poorly understood, both theoretically and empirically, despite its relevance to many fundamental concepts in evolutionary biology. In this study, we used two independent methods of estimating the heritability of lifetime female fecundity (the predominant female fitness component in this population) in a large, outbred population of Drosophila melanogaster that had adapted to the laboratory environment for over 400 generations. Despite strong directional selection on adult female fecundity, we uncovered high heritability for this trait that cannot be explained by antagonistic pleiotropy with juvenile fitness. The evolutionary significance of this high heritability of lifetime fecundity is discussed.     

Diversity and population structure of a near-shore marine-sediment viral community

Viruses, most of which are phage, are extremely abundant in marine sediments, yet almost nothing is known about their identity or diversity. We present the metagenomic analysis of an uncultured near-shore marine-sediment viral community. Three-quarters of the sequences in the sample were not related to anything previously reported. Among the sequences that could be identified, the majority belonged to double-stranded DNA phage. Temperate phage were more common than lytic phage, suggesting that lysogeny may be an important lifestyle for sediment viruses. Comparisons between the sediment sample and previously sequenced seawater viral communities showed that certain phage phylogenetic groups were abundant in all marine viral communities, while other phage groups were under-represented or absent. This 'marineness' suggests that marine phage are derived from a common set of ancestors. Several independent mathematical models, based on the distribution of overlapping shotgun sequence fragments from the library, were used to show that the diversity of the viral community was extremely high, with at least 10(4) viral genotypes per kilogram of sediment and a Shannon index greater than 9 nats. Based on these observations we propose that marine-sediment viral communities are one of the largest unexplored reservoirs of sequence space on the planet.     

Effects of rhizobial inoculation, cropping systems and growth stages on endophytic bacterial community of soybean roots

Interspecific interactions and soil nitrogen supply levels affect intercropping productivity. We hypothesized that interspecific competition can be alleviated by increasing N application rate and yield advantage can be obtained in competitive systems. A field experiment was conducted in Wuwei, Gansu province in 2007 and 2008 to study intercropping of faba bean/maize, wheat/maize, barley/maize and the corresponding monocultures of faba bean (Vicia faba L.), wheat (Triticum aestivum L.), barley (Hordeum vulgare L.) and maize (Zea mays L.) with N application rates of 0, 75, 150, 225 and 300 kg N ha^?1. Total land equivalent ratios (TLER) were 1.22 for faba bean/maize, 1.16 for wheat/maize, and 1.13 for barley/maize intercropping over the 2-year study period. Maize was overyielding when intercropped with faba bean, but underyielding when intercropped with wheat or barley according to partial land equivalent ratios (PLER) based on grain yields of individual crops in intercropping and sole cropping. There was an interspecific facilitation between intercropped faba bean and maize, and interspecific competition between maize and either wheat or barley. The underyielding of maize was higher when intercropped with barley than with wheat. Fertilizer N alleviated competitive interactions in intercrops with adequate fertilizer N at 225 kg ha^?1. Yield advantage of intercropping can be acquired with adequate nitrogen supply, even in an intensive competitive system such as barley/maize intercropping. This is important when using intercropping to develop intensive farming systems with high inputs and high outputs.