Biological nitrification inhibition (BNI)—is it a widespread phenomenon?

Regulating nitrification could be a key strategy in improving nitrogen (N) recovery and agronomic N-use efficiency in situations where the loss of N following nitrification is significant. A highly sensitive bioassay using recombinant luminescent Nitrosomonas europaea, has been developed that can detect and quantify the amount of nitrification inhibitors produced by plants (hereafter referred to as BNI activity). A number of species including tropical and temperate pastures, cereals and legumes were tested for BNI in their root exudate. There was a wide range in BNI capacity among the 18 species tested; specific BNI (AT units activity g⁻¹ root dry wt) ranged from 0 (i.e. no detectable activity) to 18.3 AT units. Among the tested cereal and legume crops, sorghum [Sorghum bicolor (L.)], pearl millet [Pennisetum glaucum (L.) R. Br.], and groundnut [Arachis hypogaea (L.)] showed detectable BNI in root exudate. Among pasture grasses, Brachiaria humidicola (Rendle) Schweick, B. decumbens Stapf showed the highest BNI capacity. Several high- and low-BNI genotypes were identified within the B. humidicola species. Soil collected from field plots of 10 year-old high-BNI genotypes of B. humidicola, showed a near total suppression (>90%) of nitrification; most of the soil inorganic N remained in the NH₄⁺ form after 30 days of incubation. In contrast, soils collected from low-BNI genotypes did not show any inhibitory effect; most of the soil inorganic N was converted to NO₃^– after 30 days of incubation. In both the high- and low-BNI genotypes, BNI was detected in root exudate only when plants were grown with NH₄⁺, but not when grown with NO₃^– as the sole source of N. BNI compounds when added to the soil inhibited nitrification and the relationship was linear (r ² = 0.92^**; n = 12). The BNI from high- and low-BNI types when added to N. europaea in pure culture, blocked both the ammonia monooxygenase (AMO) and the hydroxylamine oxidoreductase (HAO) pathways. Our results indicated that BNI capacity varies widely among and within species; and that some degree of BNI capacity is likely a widespread phenomenon in tropical pasture grasses. We suggest that the BNI capacity could either be managed and/or introduced into pastures/crops with an expression of this phenomenon, via genetic improvement approaches that combine high productivity along with some capacity to regulate soil nitrification process.     

Microsatellite mapping of genes that determine supernumerary spikelets in wheat (T. aestivum) and rye (S. cereale)

The wheat and rye spike normally bears one spikelet per rachis node, and the appearance of supernumerary spikelets is rare. The loci responsible for the ‘multirow spike’ or MRS trait in wheat, and the ‘monstrosum spike’ trait in rye were mapped by genotyping F₂ populations with microsatellite markers. Both MRS and the ‘monstrosum’ trait are under the control of a recessive allele at a single locus. The Mrs1 locus is located on chromosome 2DS, co-segregating with the microsatellite locus Xwmc453. The placement of flanking microsatellite loci into chromosome deletion bin 2DS-5 (FL 0.47–1.0) delimited the physical location of Mrs1 to the distal half of chromosome arm 2DS, within the gene rich region 2S0.8. The Mo1 locus maps about 10 cM from the centromere on chromosome arm 2RS. The similar effect on phenotype of mo1 and mrs1, together with their presence in regions of conserved synteny, suggest that they may well be members of an orthologous set of Triticeae genes governing spike branching. The practical importance of the MRS spike is that it produces more spikelets per spike, and thereby enhances the sink capacity of wheat, which is believed to limit the yield potential of the crop.     

What's in a (biological) name? The wrath of Lord Rutherford

Names in taxonomy have seven different and important properties, some due to their existence in the context of classifications. Names confer or facilitate individuation, information storage and retrieval, and set theories of relationships, explanatory power, testable predictions, conceptual power, and language. No other way of naming in science is so powerful. And this is possible because taxonomic naming is done with full consideration of the theoretical specification of empirical data (characters) and their correspondence among taxa via homology statements. Since Darwin and Hennig, sets of homologous characters distributed among taxa allow precise hypotheses of a genealogical relationship, and this relationship is reflected in the way naming results in a classification.     

X-ray photochemistry in iron complexes from Fe(0) to Fe(IV) - Can a bug become a feature?

Under intense soft X-ray irradiation, we have observed time-dependent changes in the soft X-ray spectra of virtually all the Fe coordination complexes that we have examined, indicating chemical transformation of the compound under study. Each compound, with oxidation states ranging from Fe(IV) to Fe(0), has been studied with either Fe L-edge spectroscopy or N K-edge spectroscopy. We find that very often a well-defined spectroscopic change occurs, at least initially, which is apparently capable of straightforward interpretation in terms of X-ray induced photoreduction, photooxidation or ligand photolysis. We briefly discuss the probable chemical nature of the changes and then estimate the rate of chemical change, thereby establishing the necessary radiation dose. We also demonstrate that the photochemistry not only depends on the Fe oxidation state but also the coordination chemistry of the complex. It seems that a proper understanding of such X-ray photochemical effects could well greatly assist the assignment of soft X-ray spectra of uncharacterized metal sites.     

Cloning and characterization of Methoprene-tolerant(Met)and Kruppel homolog 1(Kr-h1)genes in the wheat blossom midge,Sitodiplosis mosellana

Juvenile hormone(JH),a growth regulator,inhibits ecdysteroid-induced meta-morphosis and controls insect development and diapause.Methoprene-tolerant(Met)and Krippel homolog I(Kr-h1)are two proteins involved in JH action.To gain some insight into their function in development of Sitodiplosis mosellana,an insect pest undergoing obligatory larval diapause at the mature 3rd instar stage,we cloned full-length complemen-tary DNAs of Met and Kr-h1 from this specics.SmMet encoded a putative protein,which contained three domains typical of the bHLH-PAS family and eight conserved amino acid residues important for JH binding.SmKr-h1 encoded a protein showing high sequence homology to its counterparts in other specics,and contained all eight highly conserved Zn-finger motifs for DNA-binding.Expression patterns of SmMet and SmKr hl were de-velopmentally regulated and JH III responsive as well.Their mRNA abundance increased as larvae entered carly 3rd instar,pre-diapause and maintenance stages,and peaked during post-diapause quiescence,a pattern correlated with JH titers in this species.Different from reduced expression of SmMer,SmKr-h1 mRNA increased at mid-to-late period of post-diapause development.Topical application of JH II on diapausing larvac also induced the two genes in a dose-dependent manner.Expression of SmuMer and SmKr-h1 clearly declined in the pre-pupal phase,and was significantly higher in female adults than male adults.These results suggest that JH-responsive SmMet and SmKr-h1 might play key roles in diapause induction and maintenance as well as in post-diapause quiescence and adult reproduction,whereas metamorphosis from larvae to pupac might be correlated with their reduced expression.     

Can elevated CO(2) improve salt tolerance in olive trees?

We compared growth, leaf gas exchange characteristics, water relations, chlorophyll fluorescence, and Na⁺ and Cl⁻ concentration of two cultivars (‘Koroneiki’ and ‘Picual’) of olive (Olea europaea L.) trees in response to high salinity (NaCl 100 mM) and elevated CO₂ (eCO₂) concentration (700 μL L⁻¹). The cultivar ‘Koroneiki’ is considered to be more salt sensitive than the relatively salt-tolerant ‘Picual’. After 3 months of treatment, the 9-month-old cuttings of ‘Koroneiki’ had significantly greater shoot growth, and net CO₂ assimilation (A_CO2) at eCO₂ than at ambient CO₂, but this difference disappeared under salt stress. Growth and A_CO2 of ‘Picual’ did not respond to eCO₂ regardless of salinity treatment. Stomatal conductance (g_s) and leaf transpiration were decreased at eCO₂ such that leaf water use efficiency (WUE) increased in both cultivars regardless of saline treatment. Salt stress increased leaf Na⁺ and Cl⁻ concentration, reduced growth and leaf osmotic potential, but increased leaf turgor compared with non-salinized control plants of both cultivars. Salinity decreased A_CO2, g_s, and WUE, but internal CO₂ concentrations in the mesophyll were not affected. eCO₂ increased the sensitivity of PSII and chlorophyll concentration to salinity. eCO₂ did not affect leaf or root Na⁺ or Cl⁻ concentrations in salt-tolerant ‘Picual’, but eCO₂ decreased leaf and root Na⁺ concentration and root Cl⁻ concentration in the more salt-sensitive ‘Koroneiki’. Na⁺ and Cl⁻ accumulation was associated with the lower water use in ‘Koroneiki’ but not in ‘Picual’. Although eCO₂ increased WUE in salinized leaves and decreased salt ion uptake in the relatively salt-tolerant ‘Koroneiki’, growth of these young olive trees was not affected by eCO₂.     

Can Diversifying Selection Be Distinguished from History in Geographic Clines? A Population Genomic Study of Killifish (Fundulus heteroclitus)

A common geographical pattern of genetic variation is the one-dimensional cline. Clines may be maintained by diversifying selection across a geographical gradient but can also reflect historical processes such as allopatry followed by secondary contact. To identify loci that may be undergoing diversifying selection, we examined the distribution of geographical variation patterns across the range of the killifish (Fundulus heteroclitus) in 310 loci, including microsatellites, allozymes, and single nucleotide polymorphisms. We employed two approaches to detect loci under strong diversifying selection. First, we developed an automated method to identify clinal variation on a per-locus basis and examined the distribution of clines to detect those that exhibited signifcantly steeper slopes. Second, we employed a classic -outlier method as a complementary approach. We also assessed performance of these techniques using simulations. Overall, latitudinal clines were detected in nearly half of all loci genotyped (i.e., all eight microsatellite loci, 12 of 16 allozyme loci and 44% of the 285 SNPs). With the exception of few outlier loci (notably mtDNA and malate dehydrogenase), the positions and slopes of Fundulus clines were statistically indistinguishable. The high frequency of latitudinal clines across the genome indicates that secondary contact plays a central role in the historical demography of this species. Our simulation results indicate that accurately detecting diversifying selection using genome scans is extremely difficult in species with a strong signal of secondary contact; neutral evolution under this history produces clines as steep as those expected under selection. Based on these results, we propose that demographic history can explain all clinal patterns observed in F. heteroclitus without invoking natural selection to either establish or maintain the pattern we observe today.     

Russian wheat aphids (Diuraphis noxia) in China: native range expansion or recent introduction?

In this study, we explore the population genetics of the Russian wheat aphid (RWA) (Diuraphis noxia), one of the world's most invasive agricultural pests, in north-western China. We have analysed the data of 10 microsatellite loci and mitochondrial sequences from 27 populations sampled over 2 years in China. The results confirm that the RWAs are holocyclic in China with high genetic diversity indicating widespread sexual reproduction. Distinct differences in microsatellite genetic diversity and distribution revealed clear geographic isolation between RWA populations in northern and southern Xinjiang, China, with gene flow interrupted across extensive desert regions. Despite frequent grain transportation from north to south in this region, little evidence for RWA translocation as a result of human agricultural activities was found. Consequently, frequent gene flow among northern populations most likely resulted from natural dispersal, potentially facilitated by wind currents. We also found evidence for the long-term existence and expansion of RWAs in China, despite local opinion that it is an exotic species only present in China since 1975. Our estimated date of RWA expansion throughout China coincides with the debut of wheat domestication and cultivation practices in western Asia in the Holocene. We conclude that western China represents the limit of the far eastern native range of this species. This study is the most comprehensive molecular genetic investigation of the RWA in its native range undertaken to date and provides valuable insights into the history of the association of this aphid with domesticated cereals and wild grasses.     

Can a stench be beautiful? – Osmophores in stem-succulent stapeliads (Apocynaceae-Asclepiadoideae-Ceropegieae-Stapeliinae)

Carrion flower stapeliads are examples of olfactory mimicry, forming sapromyiophilous flowers, which mimic food sources or oviposition sites to attract fly pollinators. The aim of this work was to investigate the ultrastructure of osmophores involved in the release of the carrion odor of Orbea variegata and Boucerosia indica flowers. In spite of their similar architecture (epidermal epithelium+subepidermal secretory layers), the osmophores of stapeliads feature some differences in morphology and ultrastructure. The epidermal epithelial cells of O. variegata and B. indica differ in shape, but both are extremely rich in endoplasmic reticulum and flocculent material in the vacuole. Unlike the Orbea, Boucerosia has starchless leucoplasts in the epidermal epithelium. Orbea features a cuticle with microchannels, while Boucerosia has a different mechanism for the pathway of scent substances to the cell exterior. They are released by rupturing of the outer layer of cuticle at the apex of the papillae. The epidermal cells of the adaxial corolla differ even between parts of the corolla, the corolla lobes and the annulus in the flower. This diversity may be connected with an odor gradient. The morphological and anatomical features of stapeliad (subtribe Stapeliinae) osmophores are generally similar to osmophores of members of subtribe Ceropegiinae (Ceropegia), thus, we suggest that this model of osmophores evolved before early diversification of Ceropegieae. The ultrastructural features of stapeliad osmophores are generally similar to those of Araceae, Orchidaceae and Passifloraceae.     

In vitro tests of natural allelic variation of innate immune genes (avian β-defensins) reveal functional differences in microbial inhibition

Allelic variation in immune genes might result from, and contribute to, host-pathogen evolution. Functional allelic variation in the innate immune system has received little attention. Here, we investigate whether naturally occurring allelic variation within the avian innate immune system (β-defensins) is associated with variation in antimicrobial activity. We tested differences in in vitro antimicrobial properties of the synthesized products of two alleles of avian β-defensin 7, both of which occur at high frequency in natural populations of the great tit (Parus major). Only one allele strongly inhibited the growth of the gram-positive bacterium Staphylococcus aureus, but both alleles strongly inhibited growth of the gram-negative bacterium Escherechia coli. Our data demonstrate functional allelic variation in natural defensin genes, and we discuss how differences in efficacy against microbial species might contribute to maintaining this variation.     

Do polyphagous predators help control orange wheat blossom midge, Sitodiplosis mosellana Géhin (Dipt.,Cecidomyiidae) in winter wheat?

Abstract: Polyphagous predatory invertebrate populations were manipulated using exclusion techniques in order to examine their impact on Sitodiplosis mosellana Géhin. Experiments were conducted within the framework of the LINK Integrated Farming Systems Project in the UK, which allowed the effect of the predators to be compared between integrated and conventional farming systems. In 1995 and 1996, the exclusion technique indicated that polyphagous predators had little impact on S. mosellana numbers prior to oviposition, but may reduce the number of midge returning to the soil to diapause and thereby help to prevent populations building up in the soil. Sowing date affected ear infestation levels with earlier-drilled, conventionally farmed plots suffering heavier infestations. A strong correlation was found between the number of larvae per ear and the percentage of ears infested. At 100% infestation there was a mean of 2.8  S. mosellana larvae per ear.     

Calibration of a molecular clock in tits (Paridae)--do nucleotide substitution rates of mitochondrial genes deviate from the 2% rule?

The ongoing debate on the reliability of avian molecular clocks is actually based on only a small number of calibrations carried out under different assumptions with respect to the choice and constraints of calibration points or to the use of substitution models. In this study, we provide substitution rate estimates for two mitochondrial genes, cytochrome b and the control region, and age estimates for lineage splits within four subgenera of tits (Paridae: Parus, Cyanistes, Poecile and Periparus). Overall sequence divergence between cytochrome b lineages covers a range of 0.4-1.8% per million years and is thus consistent with the frequently adopted approximation for a sequence divergence between avian lineages of 1.6-2% per my. Overall rate variation is high and encompasses the 2% value in a 95% CI for model corrected data. Mean rate estimates for cytochrome b range between 1.9 and 8.9 x 10(-3) substitutions per site per lineage. Local rates differ significantly between taxonomic levels with lowest estimates for haplotype lineages. At the population/subspecies level mean sequence divergence between lineages matches the 2% rule best for most cytochrome b datasets (1.5-1.9% per my) with maximum estimates for small isolated populations like those of the Canarian P. teneriffae complex (up to 3.9% per my). Overall rate estimates for the control region range at similar values like those for cytochrome b (2.7-8.8 x 10(-3), 0.5-1.8% per my), however, within some subgenera mean rates are higher than those for cytochrome b for uncorrected sequence data. The lowest rates for both genes were calculated for coal tits of subgenus Periparus (0.04-0.6% per my). Model-corrected sequence data tend to result in higher rate estimates than uncorrected data. Increase of the gamma shape parameter goes along with a significant decrease of rate and partly age estimates, too. Divergence times for earliest deep splits within tit subgenera Periparus and Parus were dated to the mid Miocene at 10-14my bp. Most recent splits between east and west Palearctic taxa of blue, willow and great tits were dated to the Pliocene/Pleistocene boundary with the earliest estimates based on model-corrected trees. Relaxation of the Messinian calibration point leads to more recent divergence times for North African coal and blue tit populations during the mid Pliocene. Despite a relatively broad age constraint for the split between Nearctic and Palearctic Poecile due to the Pliocene re-opening of the Bering Strait, the split between chickadees and willow tits is dated considerably earlier than in former studies to the upper bound of the age constraint at 7.4 my BP.     

Shrinking genomes? Evidence from genome size variation in Crepis (Compositae)

Large-scale surveys of genome size evolution in angiosperms show that the ancestral genome was most likely small, with a tendency towards an increase in DNA content during evolution. Due to polyploidisation and self-replicating DNA elements, angiosperm genomes were considered to have a 'one-way ticket to obesity' (Bennetzen & Kellogg 1997). New findings on how organisms can lose DNA challenged the hypotheses of unidirectional evolution of genome size. The present study is based on the classical work of Babcock (1947a) on karyotype evolution within Crepis and analyses karyotypic diversification within the genus in a phylogenetic context. Genome size of 21 Crepis species was estimated using flow cytometry. Additional data of 17 further species were taken from the literature. Within 30 diploid Crepis species there is a striking trend towards genome contraction. The direction of genome size evolution was analysed by reconstructing ancestral character states on a molecular phylogeny based on ITS sequence data. DNA content is correlated to distributional aspects as well as life form. Genome size is significantly higher in perennials than in annuals. Within sampled species, very small genomes are only present in Mediterranean or European species, whereas their Central and East Asian relatives have larger 1C values.     

Epichlo? festucae var. lolii endophyte affects host response to fungal disease progression in perennial ryegrass (Lolium perenne)

正Dear Editor,Perennial ryegrass (Lolium perenne) is a globally important forage and turf grass species that commonly forms symbiotic associations with the asexual fungal endophyte—Epichlo? festucae var. lolii. Epichlo? endophytes mutualistically interact with host plants by providing major fitness enhancements and protection from both biotic and abiotic stresses     

Enhanced biological removal of NOχ from flue gas in a biofilter by Fe(II)Cit/Fe(II)EDTA absorption

A mixed absorbent had been proposed to enhance the chemical absorption-biological reduction process for NO_x removal from flue gas. The mole ratio of the absorbent of Fe(II)Cit to Fe(II)EDTA was selected to be 3. After the biofilm was formed adequately, some influential factors, such as the concentration of NO, O₂, SO₂ and EBRT were investigated. During the long-term running, the system could keep on a steady NO removal efficiency (up to 90%) and had a flexibility in the sudden changes of operating conditions when the simulated flue gas contained 100-500 ppm NO, 100-800 ppm SO₂, 1-5% (v/v) O₂, and 15% (v/v) CO₂. However, high NO concentration (>800 ppm) and relative short EBRT (<100 s) had significant negative effect on NO removal. The results indicate that the new system by using mixed-absorbent can reduce operating costs in comparison with the single Fe(II)EDTA system and possesses great potential for scale-up to industrial applications.     

Prevalence of virulence and extended-spectrum β-lactamase (ESBL) genes harbouring Vibrio spp. isolated from cockles (Tegillarca granosa) marketed in Korea

This study aimed to examine incidence, virulence and antimicrobial properties in Aeromonas spp. isolated from cockles (Tegillarca granosa) in Korea. Firstly, genomic DNA was extracted from 32 Aeromonas spp. isolates, and PCR screening for virulence, antimicrobial resistance genes was carried out. The disk diffusion assay was used to examine antimicrobial susceptibility. Aeromonas spp. isolates comprised, A. hydrophila (n = 8), A. veronii (n = 15), A. media (n = 2), A. salmonicida (n = 2), A. allosaccharophila (n = 1), A. bestiarum (n = 1), A. culicicola (n = 1), A. enteropelogenes (n = 1) and A. rivipollensis (n = 1). High prevalence of virulence-related genes reported as; act (69%), alt (47%), ast (41%), aerA (56%), lip (50%), ahyB (47%), ser (28%), fla (66%), gcat (44%), ascV (50%) and hlyA (72%). All isolates were multidrug resistant, while highest resistance level observed for ampicillin (100%), followed by imipenem (81%), rifampicin (78%), cephalothin (72%), piperacillin (47%) and Colistin sulfate (31%). The presence of bla_SHV, bla_CTX, tetE, aac(6’)-Ib, strA-strB, qnrS, qnrB and IntI1 genes were reported in varying combinations. Nevertheless, bla_TEM, bla_IMP, tetA, tetB, qnrA, qnrB and aphAI-IAB genes and the class1 integron were not detected. The high occurrence of virulence and antimicrobial resistance genes in cockles reveals that it can be a potential health risk source for consumers.     

Can Biomethane Potential (BMP) Be Predicted from Other Variables Such As Biochemical Composition in Lignocellulosic Biomass and Related Organic Residues?

The potential of methane production by anaerobic digestion of lignocellulosic biomass depends not only on the availability of the resources in the considered territory, but also on their physico-chemical characteristics. Relevant methods of characterization are, therefore, needed to select and possibly combine the most appropriate biomass substrates in order to optimize energy recovery through anaerobic digestion processes. The objective of the present study was to determine whether biomethane potential of such substrates could be predicted from a limited number of variables more rapidly or determined more easily. A set of 36 biomass substrates and organic residues from a variety of origins was analyzed for total and easily hydrosoluble organic matter fractions (volatile solid, VS and soluble chemical oxygen demand, SCOD), neutral detergent soluble fraction (SOL), hemicelluloses (HEM), cellulose (CELL), and lignin-like residual fractions (RES). Bioreactivity of all samples was also measured by experimental assays (biochemical oxygen demand, BOD and biochemical methane potential, BMP). The whole set of data thereby obtained was analyzed statistically considering one dependent variable (BMP), and six independent variables (SCOD, SOL, HEM, CELL, RES, and BOD). Partial least square (PLS) analysis revealed very clearly a positive correlation between BMP and BOD, which were both anti-correlated with RES. On the other hand, no correlations were observed between BMP, SCOD, HEM, and CELL contents. PLS analysis showed that BMP was significantly correlated to the six independent variables. The most influential variables were found to be RES and BOD, and a polynomial model was successfully validated for the prediction of BMP from RES and BOD.